[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/15087329/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/15098590/transformed.cor.cli.txt"

nPatients in clinical file=489, in cluster file=492, common to both=482
[1]  65 482
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         38                         444 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         38                         444 
[1] "AMP PEAK  2(3Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           72                           410 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           72                           410 
[1] "AMP PEAK  3(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           83                           399 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           83                           399 
[1] "AMP PEAK  4(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           19                           463 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           19                           463 
[1] "AMP PEAK  5(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           22                           460 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           22                           460 
[1] "AMP PEAK  6(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           28                           454 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           28                           454 
[1] "AMP PEAK  7(7P14.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                          101                           381 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                          101                           381 
[1] "AMP PEAK  8(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           98                           384 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           98                           384 
[1] "AMP PEAK  9(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            66                            416 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            66                            416 
[1] "AMP PEAK 10(8Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          152                           330 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          152                           330 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           148                            334 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           148                            334 
[1] "AMP PEAK 12(9Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           58                           424 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           58                           424 
[1] "AMP PEAK 13(11Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            46                            436 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            46                            436 
[1] "AMP PEAK 14(12Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            36                            446 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            36                            446 
[1] "AMP PEAK 15(13Q12.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             25                             457 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             25                             457 
[1] "AMP PEAK 16(14Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            27                            455 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            27                            455 
[1] "AMP PEAK 17(15Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                            15                            467 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                            15                            467 
[1] "AMP PEAK 18(16Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            29                            453 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            29                            453 
[1] "AMP PEAK 19(17Q23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            24                            458 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            24                            458 
[1] "AMP PEAK 20(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             17                             465 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             17                             465 
[1] "AMP PEAK 21(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            42                            440 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            42                            440 
[1] "AMP PEAK 22(XP22.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            24                            458 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            24                            458 
[1] "AMP PEAK 23(XP22.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            23                            459 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            23                            459 
[1] "AMP PEAK 24(XP21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           22                           460 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           22                           460 
[1] "AMP PEAK 25(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           15                           467 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           15                           467 
[1] "AMP PEAK 26(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           13                           469 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           13                           469 
[1] "AMP PEAK 27(XQ25) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         17                         465 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         17                         465 
[1] "AMP PEAK 28(XQ27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           17                           465 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           17                           465 
[1] "DEL PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           57                           425 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           57                           425 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           55                           427 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           55                           427 
[1] "DEL PEAK  3(1Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           28                           454 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           28                           454 
[1] "DEL PEAK  4(1Q42.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           46                           436 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           46                           436 
[1] "DEL PEAK  5(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         45                         437 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         45                         437 
[1] "DEL PEAK  6(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           90                           392 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           90                           392 
[1] "DEL PEAK  7(2Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           83                           399 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           83                           399 
[1] "DEL PEAK  8(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         77                         405 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         77                         405 
[1] "DEL PEAK  9(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         32                         450 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         32                         450 
[1] "DEL PEAK 10(4Q28.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           49                           433 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           49                           433 
[1] "DEL PEAK 11(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           96                           386 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           96                           386 
[1] "DEL PEAK 12(5Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           96                           386 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           96                           386 
[1] "DEL PEAK 13(5Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          105                           377 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          105                           377 
[1] "DEL PEAK 14(6P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           41                           441 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           41                           441 
[1] "DEL PEAK 15(6Q14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          173                           309 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          173                           309 
[1] "DEL PEAK 16(7Q31.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            28                            454 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            28                            454 
[1] "DEL PEAK 17(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          218                           264 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          218                           264 
[1] "DEL PEAK 18(8P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          286                           196 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          286                           196 
[1] "DEL PEAK 19(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         43                         439 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         43                         439 
[1] "DEL PEAK 20(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            152                             330 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            152                             330 
[1] "DEL PEAK 21(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            34                            448 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            34                            448 
[1] "DEL PEAK 22(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            43                            439 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            43                            439 
[1] "DEL PEAK 23(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            48                            434 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            48                            434 
[1] "DEL PEAK 24(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                           122                            360 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                           122                            360 
[1] "DEL PEAK 25(12Q24.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             42                             440 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             42                             440 
[1] "DEL PEAK 26(13Q14.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            221                             261 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            221                             261 
[1] "DEL PEAK 27(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           169                            313 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           169                            313 
[1] "DEL PEAK 28(15Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            66                            416 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            66                            416 
[1] "DEL PEAK 29(16Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           185                            297 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           185                            297 
[1] "DEL PEAK 30(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           206                            276 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           206                            276 
[1] "DEL PEAK 31(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           154                            328 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           154                            328 
[1] "DEL PEAK 32(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             93                             389 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             93                             389 
[1] "DEL PEAK 33(18Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                            126                             356 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                            126                             356 
[1] "DEL PEAK 34(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         132                          350 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         132                          350 
[1] "DEL PEAK 35(19Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            49                            433 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            49                            433 
[1] "DEL PEAK 36(21Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            50                            432 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            50                            432 
[1] "DEL PEAK 37(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           145                            337 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           145                            337 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[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] "BATCH_NUMBER"                          

Input Data has 29 rows and 482 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=427,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=12,	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.
[1] "HIGHEST_GLEASON_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=207,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=203,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 25:'PSA_VALUE':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=375,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'BATCH_NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 482 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "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"                     
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
188 281  10 
[1] "table(vv)"
vv
 T2  T3  T4 
188 281  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
188 281  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
188 281  10 
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=12, 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=207, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=109, 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    38   0
  AMP PEAK  1(1Q22) WILD-TYPE 435   8
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         38                         443 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                          0                           8 
$`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-EJ-A7NM TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6362 TCGA-G9-6363 
       21.96         4.21        15.42        13.45        47.44        45.30 
TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-7232 TCGA-HC-8265 TCGA-HI-7168 TCGA-J9-A52E 
       50.73        36.36        38.17        15.88        78.61        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KK-A8I4 TCGA-KK-A8ID TCGA-M7-A725 TCGA-V1-A9O5 
       13.32        15.22        67.99        69.27        18.84        58.39 
TCGA-V1-A9O7 TCGA-VN-A88K TCGA-VN-A88Q TCGA-VP-A875 TCGA-XJ-A9DX TCGA-XK-AAIV 
       79.73        25.51        44.91        75.91        31.99        37.25 
TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8SR TCGA-ZG-A9KY TCGA-ZG-A9L5 TCGA-ZG-A9LS 
        4.87        48.72         8.98         4.27        29.85        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.16        22.75 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       60.23        46.55        47.80        51.88        68.35        43.07 
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 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       25.18        21.60        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.58         6.48        15.65        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB 
        8.75         4.54         4.31         4.77        28.41        22.36 
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        83.87        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-G9-6364 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        58.45        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        64.18        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.93        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       40.08         1.68         2.37        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58         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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CN 
       11.77        13.55        27.12        13.87         5.85        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        67.43        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58        22.55         6.64         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78        16.31       111.39       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        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        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       47.15        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI 
       32.45       114.38        71.34        62.79        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU 
       22.59        20.28        19.17        12.43         3.78        19.04 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       1.02                        0.72 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      79.73                      165.17 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     27.765                      26.660 
[1] "1.0 - 79.7 (27.8)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "7.7e+07"
D1V2, continuous
                             vv
clus                           T2  T3  T4
  AMP PEAK  1(1Q22) MUTATED     4  29   5
  AMP PEAK  1(1Q22) WILD-TYPE 184 252   5
D1V3, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  T2                         4                         184
  T3                        29                         252
  T4                         5                           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"
D1V4, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    21  14
  AMP PEAK  1(1Q22) WILD-TYPE 317  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     21   14
  AMP PEAK  1(1Q22) WILD-TYPE  317   61
   clus
vv  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  0                        21                         317
  1                        14                          61
[1] 2 2
[1] FALSE
D1V5, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED     4  34
  AMP PEAK  1(1Q22) WILD-TYPE  10 434
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      4   34
  AMP PEAK  1(1Q22) WILD-TYPE   10  434
                                        clus
vv                                       AMP PEAK  1(1Q22) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           34
                                        clus
vv                                       AMP PEAK  1(1Q22) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            434
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  1(1Q22) MUTATED    18  19   0   0
  AMP PEAK  1(1Q22) WILD-TYPE 292 119   5  15
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  R0                        18                         292
  R1                        19                         119
  R2                         0                           5
  RX                         0                          15
[1] 4 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    69   3
  AMP PEAK  2(3Q21.3) WILD-TYPE 404   5
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           72                           409 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                            3                             5 
$`AMP PEAK  2(3Q21.3) MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5514 
       11.51        35.01        13.02        26.99        33.01        36.23 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7330 TCGA-EJ-7782 
       52.27        51.88        39.75        41.85         6.28        38.37 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-A65F TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 
       77.16        76.41        18.41        14.83         7.56        15.42 
TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-A9S0 
       13.45        66.67        45.30        50.73        30.97        26.01 
TCGA-HC-7210 TCGA-HC-7819 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
       28.54        17.85        22.42        15.88         0.76         1.78 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A76W TCGA-HC-A8CY TCGA-J4-8200 TCGA-J4-AATZ 
        2.33         1.45         7.00         9.53        12.30        13.55 
TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IA TCGA-KK-A8IB 
       44.68        54.54        29.56        20.94        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IK TCGA-V1-A8WV 
       67.43        69.27        26.43       113.98        51.39        22.55 
TCGA-V1-A9O7 TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87H TCGA-XJ-A83G 
       79.73        25.78       111.39        75.91        21.80        38.04 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SP 
       31.99        37.25         4.87        48.72        62.14        71.34 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.04        53.36        60.99         4.27        11.67        37.94 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9MC TCGA-ZG-A9NI 
       29.85        20.28        19.17         3.78        14.96         4.34 

$`AMP PEAK  2(3Q21.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-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-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-5519 TCGA-EJ-5522 
       38.53        60.23        46.55        47.80        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       43.07        36.66        38.76        60.23        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       27.68        24.39        23.90        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-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       23.05        19.92        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A6RC 
       23.34        12.92        13.71        21.90        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.77        28.41        22.36        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        83.87        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-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        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        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       64.18        52.93        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        23.93         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-7211 
       65.26         2.93        36.36        37.35        14.47         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
       30.51        30.84        24.56        31.43        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.58         1.15        22.36         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 
       17.42         3.48         1.25         4.41         4.93        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57       113.10        56.28        86.40       115.86        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       51.68        49.94        32.84        34.95        36.13        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IG 
      101.79        21.96        65.82        31.79        32.91        82.36 
TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       66.18        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       15.58         6.64        58.39         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       41.42        44.91        16.31       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       85.18        55.56        60.92        66.97        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW 
       42.08        48.03         9.04         2.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       32.19        25.48        52.96        49.02        51.45        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ 
       53.06        45.86        46.29        32.45       114.38        62.79 
TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
        8.98        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM 
       14.53        13.28        10.13        36.43        22.59        12.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       16.96        19.04        12.16        22.75        17.98        11.47 
TCGA-ZG-A9ND 
       13.48 

  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                       113.98                        165.17 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                       27.765                        26.300 
[1] "0.8 - 114.0 (27.8)" "0.7 - 165.2 (26.3)"
[1] "hr=" "3.8"
D2V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  2(3Q21.3) MUTATED    12  55   5
  AMP PEAK  2(3Q21.3) WILD-TYPE 176 226   5
D2V3, multiclass
    clus
vv   AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  T2                          12                           176
  T3                          55                           226
  T4                           5                             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"
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(3Q21.3) MUTATED    47  22
  AMP PEAK  2(3Q21.3) WILD-TYPE 291  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(3Q21.3) MUTATED     47   22
  AMP PEAK  2(3Q21.3) WILD-TYPE  291   53
   clus
vv  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  0                          47                           291
  1                          22                            53
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(3Q21.3) MUTATED     4  68
  AMP PEAK  2(3Q21.3) WILD-TYPE  10 400
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(3Q21.3) MUTATED      4   68
  AMP PEAK  2(3Q21.3) WILD-TYPE   10  400
                                        clus
vv                                       AMP PEAK  2(3Q21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             68
                                        clus
vv                                       AMP PEAK  2(3Q21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              400
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(3Q21.3) MUTATED    31  31   2   5
  AMP PEAK  2(3Q21.3) WILD-TYPE 279 107   3  10
D2V6, multiclass
    clus
vv   AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  R0                          31                           279
  R1                          31                           107
  R2                           2                             3
  RX                           5                            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"
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    80   3
  AMP PEAK  3(3Q26.2) WILD-TYPE 393   5
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           83                           398 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                            3                             5 
$`AMP PEAK  3(3Q26.2) MUTATED`
TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5771 TCGA-CH-5788 
       11.51        22.06        35.01         2.04        13.02        26.99 
TCGA-CH-5791 TCGA-EJ-5497 TCGA-EJ-5505 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5518 
       33.01        13.32        30.31        36.69        36.23        52.27 
TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7330 TCGA-EJ-7782 
       51.88        39.75        41.85        29.06         6.28        38.37 
TCGA-EJ-7792 TCGA-EJ-8468 TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 
       17.29        77.16        21.96        14.83         7.56        15.42 
TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6366 TCGA-G9-6499 TCGA-G9-7521 
       13.45        66.67        45.30         3.32        50.73        30.97 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7211 TCGA-HC-7819 TCGA-HC-8216 TCGA-HC-A4ZV 
       26.01        23.93         0.79        17.85        22.42         0.76 
TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A76W TCGA-HC-A8CY TCGA-J4-8200 
        1.78         2.33         1.45         7.00         9.53        12.30 
TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A8CM TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A7B3 
       13.55        13.87        15.22        44.68        54.54        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IK 
       20.94        63.48        67.43        26.43       113.98        51.39 
TCGA-V1-A8MU TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-VN-A88R 
       53.16        58.39        79.73         4.27         6.15        25.78 
TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJT 
      111.39        21.80        38.04        31.99        37.25        47.15 
TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SP TCGA-YL-A9WH 
        4.87        62.14        60.56        46.29        71.34        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L5 
       53.36        60.99         4.27        11.67        37.94        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9MC TCGA-ZG-A9NI 
       20.28        19.17         3.78        14.96         4.34 

$`AMP PEAK  3(3Q26.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         2.99         6.97 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         0.92        44.02        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-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       15.98         9.99        32.02         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-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        28.93        27.19        23.90        38.93        48.13 
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-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 
       68.35        43.07        36.66        38.76        60.23        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       27.68        24.39        23.90        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        14.14        18.15        19.59         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A6RC 
       12.92        13.71        18.41        21.90        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.77        28.41        22.36        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        83.87        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-G9-6364 TCGA-G9-6365 TCGA-G9-6367 
       47.15        46.52        47.44        39.39        44.81        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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        35.34        28.18        32.68 
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        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 
       36.36        37.35        14.47        28.54        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        31.43        19.36        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        1.15        22.36         2.01         2.20         1.61        17.42 
TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        3.48         1.25         4.41         4.93        25.48        18.84 
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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP 
       27.12         5.85        10.62        13.32        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       86.40       115.86        30.02       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       31.79        32.91         2.73        69.27        82.36        66.18 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        39.29        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
        6.64         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       12.20        15.65         8.42         5.59        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 
       15.52        15.81        41.42        44.91        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        37.05        42.08        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        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       36.95        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       51.45        48.72        71.77        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        32.45       114.38 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       62.79         8.98        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L4 TCGA-ZG-A9L6 
        3.09        14.53        13.28        10.13        36.43        22.59 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       12.43        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       113.98                        165.17 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       26.010                        27.055 
[1] "0.8 - 114.0 (26.0)" "0.7 - 165.2 (27.1)"
[1] "hr=" "3.7"
D3V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  3(3Q26.2) MUTATED    16  61   6
  AMP PEAK  3(3Q26.2) WILD-TYPE 172 220   4
D3V3, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  T2                          16                           172
  T3                          61                           220
  T4                           6                             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"
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED    54  25
  AMP PEAK  3(3Q26.2) WILD-TYPE 284  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED     54   25
  AMP PEAK  3(3Q26.2) WILD-TYPE  284   50
   clus
vv  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  0                          54                           284
  1                          25                            50
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED     4  79
  AMP PEAK  3(3Q26.2) WILD-TYPE  10 389
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED      4   79
  AMP PEAK  3(3Q26.2) WILD-TYPE   10  389
                                        clus
vv                                       AMP PEAK  3(3Q26.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             79
                                        clus
vv                                       AMP PEAK  3(3Q26.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              389
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(3Q26.2) MUTATED    36  38   2   4
  AMP PEAK  3(3Q26.2) WILD-TYPE 274 100   3  11
D3V6, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  R0                          36                           274
  R1                          38                           100
  R2                           2                             3
  RX                           4                            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"
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    19   0
  AMP PEAK  4(4P16.3) WILD-TYPE 454   8
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           19                           462 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                            0                             8 
$`AMP PEAK  4(4P16.3) MUTATED`
TCGA-CH-5751 TCGA-EJ-5521 TCGA-EJ-5542 TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-A46G 
       35.01        51.88        29.06        76.41        24.85        21.96 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-8265 TCGA-J9-A8CL TCGA-KK-A8I4 TCGA-KK-A8ID 
       39.95        50.73        15.88        13.32        67.99        69.27 
TCGA-M7-A724 TCGA-V1-A9Z7 TCGA-VP-A875 TCGA-XJ-A9DX TCGA-YL-A8HO TCGA-YL-A8SR 
       29.23         4.27        75.91        31.99        71.77         8.98 
TCGA-ZG-A9KY 
        4.27 

$`AMP PEAK  4(4P16.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        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-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-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-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        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        77.16 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        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 
       83.87        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-G9-6370 TCGA-G9-6371 
       39.39        44.81         3.32        40.18        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        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        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        23.93 
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        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        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 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 
       32.84        34.95        36.13        29.56        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       13.15        34.85        25.08        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78        16.31       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
        4.87        52.96        49.02        51.45        48.72        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79        14.04        53.36        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         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                         4.27                          0.72 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                        76.41                        165.17 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                        31.99                         26.17 
[1] "4.3 - 76.4 (32.0)"  "0.7 - 165.2 (26.2)"
[1] "hr="     "2.7e+07"
D4V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  4(4P16.3) MUTATED     1  16   2
  AMP PEAK  4(4P16.3) WILD-TYPE 187 265   8
D4V3, multiclass
    clus
vv   AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  T2                           1                           187
  T3                          16                           265
  T4                           2                             8
[1] 3 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    13   5
  AMP PEAK  4(4P16.3) WILD-TYPE 325  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4P16.3) MUTATED     13    5
  AMP PEAK  4(4P16.3) WILD-TYPE  325   70
   clus
vv  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  0                          13                           325
  1                           5                            70
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(4P16.3) MUTATED     1  18
  AMP PEAK  4(4P16.3) WILD-TYPE  13 450
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4P16.3) MUTATED      1   18
  AMP PEAK  4(4P16.3) WILD-TYPE   13  450
                                        clus
vv                                       AMP PEAK  4(4P16.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             18
                                        clus
vv                                       AMP PEAK  4(4P16.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              450
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(4P16.3) MUTATED     9   9   0   1
  AMP PEAK  4(4P16.3) WILD-TYPE 301 129   5  14
D4V6, multiclass
    clus
vv   AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  R0                           9                           301
  R1                           9                           129
  R2                           0                             5
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    22   0
  AMP PEAK  5(4Q13.3) WILD-TYPE 451   8
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           22                           459 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                            0                             8 
$`AMP PEAK  5(4Q13.3) MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-KK-A6E1 TCGA-KK-A8I4 
       11.51        35.01        36.66        29.06        54.54        67.99 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-M7-A724 TCGA-VN-A88N TCGA-VP-A875 TCGA-XJ-A9DX 
       69.27        26.43        29.23        15.52        75.91        31.99 
TCGA-XK-AAJT TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8S8 TCGA-YL-A9WI TCGA-ZG-A9KY 
       47.15         4.87        49.02        62.14        53.36         4.27 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9N3 
        3.78        16.96        12.16        11.47 

$`AMP PEAK  5(4Q13.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-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-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-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        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-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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        83.87        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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        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        23.93         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        65.26         2.93        36.36        37.35 
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        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       86.40       115.86        30.02       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53         6.21        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31       111.39       109.58        97.41        23.93        85.18 
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        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       38.04        42.08        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 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM 
       51.81        32.19        25.48        52.96        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       71.77        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         8.98        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         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       10.13        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       20.28        19.17        12.43        19.04        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                         3.78                          0.72 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                        75.91                        165.17 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                        30.61                         26.04 
[1] "3.8 - 75.9 (30.6)"  "0.7 - 165.2 (26.0)"
[1] "hr="     "2.7e+07"
D5V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  5(4Q13.3) MUTATED     2  18   2
  AMP PEAK  5(4Q13.3) WILD-TYPE 186 263   8
D5V3, multiclass
    clus
vv   AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  T2                           2                           186
  T3                          18                           263
  T4                           2                             8
[1] 3 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    11  11
  AMP PEAK  5(4Q13.3) WILD-TYPE 327  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(4Q13.3) MUTATED     11   11
  AMP PEAK  5(4Q13.3) WILD-TYPE  327   64
   clus
vv  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  0                          11                           327
  1                          11                            64
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(4Q13.3) MUTATED     1  21
  AMP PEAK  5(4Q13.3) WILD-TYPE  13 447
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(4Q13.3) MUTATED      1   21
  AMP PEAK  5(4Q13.3) WILD-TYPE   13  447
                                        clus
vv                                       AMP PEAK  5(4Q13.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             21
                                        clus
vv                                       AMP PEAK  5(4Q13.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              447
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(4Q13.3) MUTATED     7  14   0   1
  AMP PEAK  5(4Q13.3) WILD-TYPE 303 124   5  14
D5V6, multiclass
    clus
vv   AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  R0                           7                           303
  R1                          14                           124
  R2                           0                             5
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    28   0
  AMP PEAK  6(5Q35.3) WILD-TYPE 445   8
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           28                           453 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                            0                             8 
$`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        21.96        15.88 
TCGA-HI-7168 TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KK-A59Z TCGA-KK-A7B2 
       78.61        10.62        13.32        15.22        86.40        36.13 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID TCGA-V1-A9OH 
       20.94        67.99        63.48         2.73        69.27        41.19 
TCGA-VN-A88K TCGA-VP-A875 TCGA-VP-A87H TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SL 
       25.51        75.91        21.80        71.77        62.14        32.45 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9NI 
       10.13         4.27        11.67         4.34 

$`AMP PEAK  6(5Q35.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5519 TCGA-EJ-5522 TCGA-EJ-5524 
       60.23        46.55        47.80        64.50        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        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        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        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        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        83.87        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        58.45 
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        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        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        23.93         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        65.26         2.93        36.36        37.35        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        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 
        2.27        22.55        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 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       27.12        13.87         5.85        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       34.95        29.56       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       32.91        67.43        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        5.82         8.84        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       41.42        44.91        25.78        16.31       111.39       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        45.86        46.29       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L2 
       49.91        28.34         3.09        14.53        13.28        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       14.96        11.47        13.48 

  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                         2.73                          0.72 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                        86.40                        165.17 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                        28.98                         26.66 
[1] "2.7 - 86.4 (29.0)"  "0.7 - 165.2 (26.7)"
[1] "hr="     "2.8e+07"
D6V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  6(5Q35.3) MUTATED     2  24   2
  AMP PEAK  6(5Q35.3) WILD-TYPE 186 257   8
D6V3, multiclass
    clus
vv   AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  T2                           2                           186
  T3                          24                           257
  T4                           2                             8
[1] 3 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    14  12
  AMP PEAK  6(5Q35.3) WILD-TYPE 324  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5Q35.3) MUTATED     14   12
  AMP PEAK  6(5Q35.3) WILD-TYPE  324   63
   clus
vv  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  0                          14                           324
  1                          12                            63
[1] 2 2
[1] FALSE
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(5Q35.3) MUTATED     1  27
  AMP PEAK  6(5Q35.3) WILD-TYPE  13 441
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5Q35.3) MUTATED      1   27
  AMP PEAK  6(5Q35.3) WILD-TYPE   13  441
                                        clus
vv                                       AMP PEAK  6(5Q35.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             27
                                        clus
vv                                       AMP PEAK  6(5Q35.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              441
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5Q35.3) MUTATED    13  13   1   1
  AMP PEAK  6(5Q35.3) WILD-TYPE 297 125   4  14
D6V6, multiclass
    clus
vv   AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  R0                          13                           297
  R1                          13                           125
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   100   1
  AMP PEAK  7(7P14.3) WILD-TYPE 373   7
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                          101                           380 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                            1                             7 
$`AMP PEAK  7(7P14.3) MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5768 TCGA-CH-5771 
       11.51        35.01         2.04        44.02        24.03        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 
       15.98        26.99        33.01        27.16        33.11        48.13 
TCGA-EJ-5542 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 
       29.06        93.70        37.81         6.28        25.68        14.53 
TCGA-EJ-7789 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-AB20 
       18.15        25.74         7.56        15.58        10.82         4.31 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6377 
       15.42        13.45        66.67         3.32        40.31        31.50 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7213 
       56.75        64.18        50.73        28.18        65.26        40.08 
TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
        1.48        22.55        17.95        15.88         0.76         1.78 
TCGA-HC-A6AP TCGA-HC-A76W TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J9-A52E 
        2.33         7.00        78.61        43.69        20.19        10.62 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AY 
       13.32        40.67        86.40        58.19         6.44        51.68 
TCGA-KK-A7B0 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF 
       32.84        20.94        67.99        63.48         2.73        26.43 
TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A721 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8MG 
       82.36        51.39        13.15        41.00        13.32        28.18 
TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9OX TCGA-V1-A9ZI TCGA-VN-A88P 
       52.08        22.55        79.73         8.42         4.70        41.42 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ 
      111.39        75.91        85.18        21.80        44.88        45.47 
TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAJ3 TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO 
       42.08        31.99        41.49         4.87        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       62.14        56.52        45.14        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9LB 
       53.36        62.37        14.53         4.27        11.67        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.43        22.75        17.98        11.47         4.34 

$`AMP PEAK  7(7P14.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-5761 TCGA-CH-5763 
        1.02        13.02        31.00         1.02         0.92        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5789 
        1.02        23.01         1.02        15.06         2.04         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       32.02         2.99        29.00        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-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        23.90        38.93        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-7115 TCGA-EJ-7123 TCGA-EJ-7218 
       60.23        41.85        47.87        88.34        74.10        83.57 
TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       36.13        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68        24.39        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       20.55        14.14        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        20.58        17.23        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 
        4.21         9.27         9.83         8.75         4.54         4.77 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        22.36        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        83.87        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-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       39.95        38.01        26.66        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       27.29        58.22        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        32.68        26.01        23.93         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        36.36        37.35        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        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       44.55         0.72         2.10        31.69        23.57         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8262 
       22.42        28.27        23.87         2.17         2.27        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.58         1.15        22.36         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         3.48         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 
        9.53        25.48        18.84        88.24        82.92        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM 
       11.77        13.55        27.12        13.87         5.85        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
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       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ 
       67.59       115.13        49.25       113.33        67.07        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       58.36        27.02        34.65        49.94        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       29.56       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       67.43        69.27        66.18       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 
       47.28         5.19        21.14        12.62        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        11.90        41.23        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       14.73        39.29        53.16        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       58.39         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       12.20        15.65         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       49.87         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.52        15.81        44.91        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       97.41        23.93        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       42.94        14.76        32.19         3.91        37.05        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        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 TCGA-YL-A8SA 
       25.48        52.96        49.02        51.45        60.56        16.83 
TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
      114.38        71.34        60.99        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        3.09        13.28        10.13        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        20.28         3.78        16.96        19.04        12.16 
TCGA-ZG-A9MC TCGA-ZG-A9ND 
       14.96        13.48 

  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                       111.39                        165.17 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                        26.99                         26.48 
[1] "0.8 - 111.4 (27.0)" "0.7 - 165.2 (26.5)"
[1] "hr=" "1.5"
D7V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  7(7P14.3) MUTATED    28  71   2
  AMP PEAK  7(7P14.3) WILD-TYPE 160 210   8
D7V3, multiclass
    clus
vv   AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  T2                          28                           160
  T3                          71                           210
  T4                           2                             8
[1] 3 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    71  18
  AMP PEAK  7(7P14.3) WILD-TYPE 267  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P14.3) MUTATED     71   18
  AMP PEAK  7(7P14.3) WILD-TYPE  267   57
   clus
vv  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  0                          71                           267
  1                          18                            57
[1] 2 2
[1] FALSE
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P14.3) MUTATED     2  99
  AMP PEAK  7(7P14.3) WILD-TYPE  12 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P14.3) MUTATED      2   99
  AMP PEAK  7(7P14.3) WILD-TYPE   12  369
                                        clus
vv                                       AMP PEAK  7(7P14.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             99
                                        clus
vv                                       AMP PEAK  7(7P14.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              369
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(7P14.3) MUTATED    49  44   1   4
  AMP PEAK  7(7P14.3) WILD-TYPE 261  94   4  11
D7V6, multiclass
    clus
vv   AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  R0                          49                           261
  R1                          44                            94
  R2                           1                             4
  RX                           4                            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"
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    97   1
  AMP PEAK  8(7Q22.1) WILD-TYPE 376   7
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           98                           383 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                            1                             7 
$`AMP PEAK  8(7Q22.1) MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       11.51        35.01        24.03        13.02        15.98        26.99 
TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 
       33.01        27.16        33.11        48.13        36.66        29.06 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 
       93.70        37.81         6.28        25.68        14.53        18.15 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-AB20 
       25.74        21.96         7.56        15.58        10.82         4.31 
TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 
       13.45        66.67         3.32        40.31        31.50        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 TCGA-HC-7742 TCGA-HC-8216 TCGA-HC-8260 
       64.18        50.73        28.18         1.48        22.42        22.55 
TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A76W 
       17.95        15.88         0.76         1.78         2.33         7.00 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
       78.61        43.69        20.19        10.62        13.32        40.67 
TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B4 
       86.40        58.19         6.44        51.68        32.84        20.94 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A721 TCGA-QU-A6IM 
        2.73        26.43        82.36        51.39        13.15        41.00 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9OX 
       13.32        28.18        52.08        22.55        79.73         8.42 
TCGA-V1-A9ZI TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H 
        4.70        41.42       111.39        75.91        85.18        21.80 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XK-AAJ3 TCGA-YJ-A8SW TCGA-YL-A8HM 
       44.88        45.47        42.08        41.49         4.87        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR 
       71.77        62.14        56.52       114.38        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QX TCGA-ZG-A9KY TCGA-ZG-A9L0 
       14.04        53.36        62.37        14.53         4.27        11.67 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       19.17        12.43         3.78        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       11.47         4.34 

$`AMP PEAK  8(7Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-5766 TCGA-CH-5767 
       44.02        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-5526 
       52.27        64.50        51.88        68.35        43.07        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        41.85        47.87        88.34        74.10 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        36.13        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       35.18        30.35        27.68        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       25.87        20.55        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        21.60        20.58        17.23        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 
        4.21         9.27         9.83         8.75         4.54         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42        22.36        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        83.87        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        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        52.93        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        23.93         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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       31.69        23.57         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        31.43        19.36        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 
        2.27        22.32         1.58         1.15        22.36         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        4.41         4.93         9.53        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       82.92        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
        5.85        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57       113.10        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       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ 
       67.07        52.93        58.36        27.02        34.65        49.94 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        67.43        69.27 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       21.14        12.62        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       11.90        41.23        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 
       53.16        30.38        15.58         6.64        58.39         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR 
        5.59         4.27         6.15        17.75        49.87         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58        97.41        23.93 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        53.36        42.94        14.76 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        37.05        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       52.96        49.02        51.45        60.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
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         3.09 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       13.28        10.13        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9ND 
       20.28        16.96        19.04        12.16        13.48 

  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                       114.38                        165.17 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                       24.855                        27.120 
[1] "0.8 - 114.4 (24.9)" "0.7 - 165.2 (27.1)"
[1] "hr=" "1.5"
D8V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  8(7Q22.1) MUTATED    29  67   2
  AMP PEAK  8(7Q22.1) WILD-TYPE 159 214   8
D8V3, multiclass
    clus
vv   AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  T2                          29                           159
  T3                          67                           214
  T4                           2                             8
[1] 3 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    69  16
  AMP PEAK  8(7Q22.1) WILD-TYPE 269  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q22.1) MUTATED     69   16
  AMP PEAK  8(7Q22.1) WILD-TYPE  269   59
   clus
vv  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  0                          69                           269
  1                          16                            59
[1] 2 2
[1] FALSE
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q22.1) MUTATED     3  95
  AMP PEAK  8(7Q22.1) WILD-TYPE  11 373
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q22.1) MUTATED      3   95
  AMP PEAK  8(7Q22.1) WILD-TYPE   11  373
                                        clus
vv                                       AMP PEAK  8(7Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             95
                                        clus
vv                                       AMP PEAK  8(7Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              373
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(7Q22.1) MUTATED    49  43   1   3
  AMP PEAK  8(7Q22.1) WILD-TYPE 261  95   4  12
D8V6, multiclass
    clus
vv   AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  R0                          49                           261
  R1                          43                            95
  R2                           1                             4
  RX                           3                            12
[1] 4 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    66   0
  AMP PEAK  9(8P11.23) WILD-TYPE 407   8
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            66                            415 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                             0                              8 
$`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-EJ-AB27 TCGA-FC-7961 
       93.70        23.90        25.68         7.56         4.77        15.42 
TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6499 TCGA-HC-7078 TCGA-HC-7210 
       13.45         3.32        26.66        50.73        65.26        28.54 
TCGA-HC-7213 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A8CL 
       40.08         1.15         0.76        78.61        13.87        13.32 
TCGA-KC-A7F6 TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A7AQ TCGA-KK-A7AV 
        8.65       113.10        86.40       115.86        52.93        27.02 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48         2.73        69.27 
TCGA-M7-A725 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A9O5 TCGA-V1-A9OA 
       18.84        41.23        28.18        39.29        58.39        20.91 
TCGA-V1-A9OL TCGA-V1-A9Z7 TCGA-VN-A943 TCGA-VP-A87H TCGA-VP-AA1N TCGA-XJ-A83G 
       19.36         4.27        16.31        21.80        44.88        38.04 
TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       31.99        47.15         4.87        48.72        71.77        62.14 
TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       46.29        62.79        53.36        62.37        11.67        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.59        19.17        12.43        22.75        13.48         4.34 

$`AMP PEAK  9(8P11.23) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        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-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-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        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        88.34        74.10 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        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        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.31        28.41        22.36        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        83.87 
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-G9-6377 
       44.81        40.18        39.95        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        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 
       64.18        52.93        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        23.93         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        36.36        37.35        14.47 
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        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A631 
       17.95        22.32         1.58        15.88        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       20.28        11.77        13.55        27.12         5.85        10.62 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       56.28        44.68        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AU TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       58.36        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       13.32        40.44        16.70        14.73        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58        22.55         6.64        79.73         6.71 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        41.19        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        85.18        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       42.08        48.03         9.04         2.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       40.04        41.49        30.58        41.39        36.95        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 
       32.19        25.48        52.96        49.02        51.45        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86        32.45       114.38        71.34         8.98        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L9 
       13.28        10.13         4.27        37.94        36.43        20.28 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        17.98        14.96 
TCGA-ZG-A9N3 
       11.47 

  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                          0.76                           0.72 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                        115.86                         165.17 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                        29.195                         25.870 
[1] "0.8 - 115.9 (29.2)" "0.7 - 165.2 (25.9)"
[1] "hr="   "9e+07"
D9V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK  9(8P11.23) MUTATED    15  48   3
  AMP PEAK  9(8P11.23) WILD-TYPE 173 233   7
D9V3, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  T2                           15                            173
  T3                           48                            233
  T4                            3                              7
[1] 3 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    48  13
  AMP PEAK  9(8P11.23) WILD-TYPE 290  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     48   13
  AMP PEAK  9(8P11.23) WILD-TYPE  290   62
   clus
vv  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  0                           48                            290
  1                           13                             62
[1] 2 2
[1] FALSE
D9V5, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED     1  65
  AMP PEAK  9(8P11.23) WILD-TYPE  13 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED      1   65
  AMP PEAK  9(8P11.23) WILD-TYPE   13  403
                                        clus
vv                                       AMP PEAK  9(8P11.23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              65
                                        clus
vv                                       AMP PEAK  9(8P11.23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               403
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8P11.23) MUTATED    31  28   1   3
  AMP PEAK  9(8P11.23) WILD-TYPE 279 110   4  12
D9V6, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  R0                           31                            279
  R1                           28                            110
  R2                            1                              4
  RX                            3                             12
[1] 4 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   149   3
  AMP PEAK 10(8Q22.1) WILD-TYPE 324   5
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          152                           329 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                            3                             5 
$`AMP PEAK 10(8Q22.1) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5739 
       32.71        22.06        33.96         3.68        11.51        22.06 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5767 
       35.01         1.02         2.04         0.92        44.02        15.06 
TCGA-CH-5771 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 
       13.02        28.93        23.90        48.13        48.53        36.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       47.80        52.27        51.88        36.66        38.76        39.75 
TCGA-EJ-5532 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7781 TCGA-EJ-7784 
       47.87        74.10        93.70        36.13        23.90        25.68 
TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65F TCGA-EJ-A65J 
       18.15        76.41        25.74        21.96        18.41        14.83 
TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-AB27 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6361 
        7.56        15.58         4.77        15.42        13.45        46.52 
TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 
        3.32        26.66        31.50        58.22        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 
       38.96        30.97        26.01        23.93        65.26        28.60 
TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-8266 
       40.08         1.48        23.70        22.42        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A8CY TCGA-HI-7168 
        0.76         2.01         2.20        17.42         9.53        78.61 
TCGA-HI-7171 TCGA-J4-A67M TCGA-J4-A83J TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A52E 
       43.69        30.94        22.88        13.55        13.87        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z 
       13.32        15.22        43.66       113.10        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      115.86        58.19         6.44        58.36        27.02        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       49.94        20.94        67.99        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK 
       63.48         2.73        69.27        26.43        82.36        51.39 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IO TCGA-V1-A8MF TCGA-V1-A8MG 
       29.23        18.84         3.19       122.17        41.23        28.18 
TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH 
       39.29        22.55        58.39        79.73        20.91        41.19 
TCGA-V1-A9OL TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-VN-A88M 
       19.36         8.42         4.27         6.15         4.70         6.21 
TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N 
       41.42        16.31        75.91        60.92        21.80        44.88 
TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YJ-A8SW 
       45.47        38.04        42.08        37.25        47.15         4.87 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SO 
       48.72        71.77        62.14        60.56        46.29       114.38 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-YL-A9WY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       28.34        11.67        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       12.43        16.96        19.04        12.16        22.75        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

$`AMP PEAK 10(8Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU 
       20.42        43.79        25.35        31.96        30.31        20.22 
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-5763 TCGA-CH-5764 
       24.03         1.02        13.02        31.00        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 
       23.01         1.02        24.03         2.04        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-5508 TCGA-EJ-5510 
       26.30        45.73        30.31        27.19        38.93        36.69 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 
       38.53        60.23        46.55        64.50        68.35        43.07 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 
       60.23        41.85        29.06        88.34        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        38.37        25.87        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-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        77.16        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       20.58        17.23        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       13.71        21.90        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
        8.75         4.54         4.31        28.41        22.36        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        83.87        55.76        18.21        68.68        49.81 
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-G9-6365 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-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 
       37.97        58.45        25.15        27.29        56.75        64.18 
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        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.54         0.79         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        31.69        23.57         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        31.43        19.36        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
       22.36         1.78         1.61         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
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        33.01        25.32 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       25.28        27.91        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CN 
       14.37        20.28        11.77        27.12         5.85        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 
       12.69        30.71        59.67        19.96        44.35        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A6E0 
        8.65        19.66         8.88        11.57        56.28        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       67.07        52.93        51.68        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IC TCGA-KK-A8IH TCGA-KK-A8II 
       29.56       101.79        21.96        67.43        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN 
       13.15        34.85        25.08         5.69        41.00       140.19 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        11.90        13.32        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       14.73        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z9 
        6.71        38.93        12.20        15.65         5.59        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       49.87         5.82         8.84        25.51        24.53        15.52 
TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       15.81        44.91        25.78       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       23.93        85.18        55.56        66.97        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A9DI TCGA-XJ-A9DK 
       14.76        32.19         3.91        37.05        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        31.99        31.96        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ 
       41.39        36.95        51.81        32.19        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       49.02        51.45        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WL 
       28.77        53.06        45.86        32.45        71.34        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9LN TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       37.94        36.43         3.78        17.98        14.96 

  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                       122.17                        165.17 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                        28.47                         25.78 
[1] "0.8 - 122.2 (28.5)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1"  
D10V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 10(8Q22.1) MUTATED    33 113   6
  AMP PEAK 10(8Q22.1) WILD-TYPE 155 168   4
D10V3, multiclass
    clus
vv   AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  T2                          33                           155
  T3                         113                           168
  T4                           6                             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"
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(8Q22.1) MUTATED   105  37
  AMP PEAK 10(8Q22.1) WILD-TYPE 233  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(8Q22.1) MUTATED    105   37
  AMP PEAK 10(8Q22.1) WILD-TYPE  233   38
   clus
vv  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  0                         105                           233
  1                          37                            38
[1] 2 2
[1] FALSE
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(8Q22.1) MUTATED     3 149
  AMP PEAK 10(8Q22.1) WILD-TYPE  11 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(8Q22.1) MUTATED      3  149
  AMP PEAK 10(8Q22.1) WILD-TYPE   11  319
                                        clus
vv                                       AMP PEAK 10(8Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            149
                                        clus
vv                                       AMP PEAK 10(8Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              319
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(8Q22.1) MUTATED    75  65   1   7
  AMP PEAK 10(8Q22.1) WILD-TYPE 235  73   4   8
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  R0                          75                           235
  R1                          65                            73
  R2                           1                             4
  RX                           7                             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"
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   146   2
  AMP PEAK 11(8Q24.21) WILD-TYPE 327   6
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           148                            333 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                             2                              6 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5739 
       32.71        22.06        33.96         3.68        11.51        22.06 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5767 
       35.01         1.02         2.04         0.92        44.02        15.06 
TCGA-CH-5771 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 
       13.02        28.93        23.90        48.13        48.53        36.23 
TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5532 
       47.80        51.88        36.66        38.76        39.75        47.87 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8469 
       74.10        93.70        23.90        25.68        18.15        76.41 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65F TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A7NH 
       25.74        21.96        18.41        14.83         7.56        15.58 
TCGA-EJ-AB27 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 
        4.77        15.42        13.45         3.32        26.66        31.50 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 
       58.22        50.73        52.93        38.96        30.97        26.01 
TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7745 
       23.93        65.26        28.60        40.08         1.48        23.70 
TCGA-HC-8216 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 
       22.42         1.58        15.88         1.15         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67M 
        2.20        17.42         9.53        78.61        43.69        30.94 
TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A4BL TCGA-KC-A4BV 
       13.55        10.62        13.32        15.22        30.71        43.66 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A7AP 
      113.10        44.68        86.40       115.86        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B4 
       52.93        58.36        27.02        34.65        49.94        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       67.99        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A724 TCGA-M7-A725 
       69.27        26.43        82.36        51.39        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IO TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8WV 
        3.19       122.17        41.23        28.18        39.29        22.55 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 
       58.39        79.73        20.91        41.19        19.36         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-VN-A88M TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 
        6.15         4.70         6.21        41.42        16.31        75.91 
TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A83H 
       60.92        21.80        44.88        45.47        38.04        42.08 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO 
       31.99        37.25        47.15         4.87        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR 
       62.14        60.56        46.29       114.38        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       14.04        53.36        62.37         4.27        11.67        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LY 
       22.59        20.28        19.17        12.43         3.78        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        11.47        13.48         4.34 

$`AMP PEAK 11(8Q24.21) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU 
       20.42        43.79        25.35        31.96        30.31        20.22 
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-5763 TCGA-CH-5764 
       24.03         1.02        13.02        31.00        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 
       23.01         1.02        24.03         2.04        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-5508 TCGA-EJ-5510 
       26.30        45.73        30.31        27.19        38.93        36.69 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       38.53        60.23        46.55        52.27        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 
       43.07        60.23        41.85        29.06        88.34        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       35.18        30.35        27.68         6.28        24.39        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-8470 TCGA-EJ-8472 
        3.75        23.05        19.92        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        21.60        20.58        17.23        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A6RC 
       23.34        12.92        13.71        21.90        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
        8.22        14.20         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-FC-7708 
        9.27         9.83         8.75         4.54         4.31        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       39.95        38.01        40.31        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       27.29        56.75        64.18        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       32.68         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 
       36.36        37.35        14.47        28.54         0.79         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
       23.57         1.68        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP 
       17.95        22.32        22.36         1.78         1.61         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
       25.48        18.84        88.24        82.92        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       33.01        25.32        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BN 
       27.12        13.87         5.85        40.67        12.69        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       19.96        44.35        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       11.57        56.28        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AY TCGA-KK-A7B0 
      115.13        49.25       113.33        67.07        51.68        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IC 
       34.95        36.13        29.56       101.79        21.96        67.43 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC 
       21.14        12.62        13.15        34.85        25.08         5.69 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       140.19        86.14        18.12        11.90        13.32 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       40.44        16.70        14.73        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT 
       15.58         6.64         6.71        38.93        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I 
        8.42         5.59        17.75        49.87         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R 
       25.51        24.53        15.52        15.81        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        53.36        42.94        14.76        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW 
       37.05        48.03         9.04         2.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        30.58        41.39        36.95        51.81        32.19 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB 
       25.48        52.96        49.02        51.45        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       41.46        45.14        28.77        53.06        45.86        32.45 
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         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9LS 
       14.53        13.28        10.13        37.94        36.43        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       19.04        17.98        14.96 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.76                           0.72 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        122.17                         165.17 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        28.765                         25.780 
[1] "0.8 - 122.2 (28.8)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1.7"
D11V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 11(8Q24.21) MUTATED    33 109   6
  AMP PEAK 11(8Q24.21) WILD-TYPE 155 172   4
D11V3, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T2                           33                            155
  T3                          109                            172
  T4                            6                              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"
D11V4, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED   100  38
  AMP PEAK 11(8Q24.21) WILD-TYPE 238  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED    100   38
  AMP PEAK 11(8Q24.21) WILD-TYPE  238   37
   clus
vv  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  0                          100                            238
  1                           38                             37
[1] 2 2
[1] FALSE
D11V5, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED     3 145
  AMP PEAK 11(8Q24.21) WILD-TYPE  11 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      3  145
  AMP PEAK 11(8Q24.21) WILD-TYPE   11  323
                                        clus
vv                                       AMP PEAK 11(8Q24.21) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             145
                                        clus
vv                                       AMP PEAK 11(8Q24.21) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               323
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(8Q24.21) MUTATED    75  61   1   7
  AMP PEAK 11(8Q24.21) WILD-TYPE 235  77   4   8
D11V6, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  R0                           75                            235
  R1                           61                             77
  R2                            1                              4
  RX                            7                              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"
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    58   0
  AMP PEAK 12(9Q33.3) WILD-TYPE 415   8
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           58                           423 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                            0                             8 
$`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-8472 TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-A4JI 
       38.76        18.15        24.85        21.96        18.41        13.45 
TCGA-G9-6356 TCGA-G9-6373 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7821 TCGA-HC-8216 
       47.15        26.66        30.97        40.08        31.43        22.42 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A8CY TCGA-HI-7168 
        1.15        22.36         0.76         1.78         9.53        78.61 
TCGA-J4-AATZ TCGA-KK-A59Z TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7B4 TCGA-KK-A8I4 
       13.55        86.40         6.44        58.36        20.94        67.99 
TCGA-KK-A8ID TCGA-V1-A8MJ TCGA-V1-A8WV TCGA-V1-A9OL TCGA-VN-A88I TCGA-VN-A88K 
       69.27        40.44        22.55        19.36         8.84        25.51 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H TCGA-X4-A8KQ TCGA-XJ-A9DX 
      111.39        75.91        60.92        21.80        45.47        31.99 
TCGA-XK-AAIV TCGA-YJ-A8SW TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SL TCGA-YL-A8SQ 
       37.25         4.87        71.77        41.46        32.45        62.79 
TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       62.37         4.27        11.67        29.85        20.28        19.17 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9NI 
        3.78        16.96        17.98         4.34 

$`AMP PEAK 12(9Q33.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        15.98        26.99         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
        2.99        29.00        27.16        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-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       51.88        68.35        43.07        36.66        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
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 
       77.16        76.41        38.10        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        15.42        22.36        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 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        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-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        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        64.18        50.73        52.93        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        23.93         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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       37.35        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        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A632 
       22.55        17.95        22.32         1.58        15.88         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       58.19        52.93        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I6 
       32.84        34.95        36.13        29.56       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        28.18        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ 
       79.73         6.71        20.91        38.93        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       49.87         4.70         5.82        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.81        41.42        44.91        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J 
       97.41        23.93        85.18        55.56        66.97        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        44.88        14.76        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       38.04        42.08        48.03         9.04         2.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       51.81        32.19        25.48        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       48.72        62.14        60.56        16.83        56.52        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29       114.38        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 
       28.34         3.09        14.53        13.28        10.13        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       36.43        22.59        12.43        19.04        12.16        22.75 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       14.96        11.47        13.48 

  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                       111.39                        165.17 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                        23.70                         27.09 
[1] "0.8 - 111.4 (23.7)" "0.7 - 165.2 (27.1)"
[1] "hr="     "8.1e+07"
D12V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 12(9Q33.3) MUTATED     5  50   3
  AMP PEAK 12(9Q33.3) WILD-TYPE 183 231   7
D12V3, multiclass
    clus
vv   AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  T2                           5                           183
  T3                          50                           231
  T4                           3                             7
[1] 3 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    29  27
  AMP PEAK 12(9Q33.3) WILD-TYPE 309  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9Q33.3) MUTATED     29   27
  AMP PEAK 12(9Q33.3) WILD-TYPE  309   48
   clus
vv  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  0                          29                           309
  1                          27                            48
[1] 2 2
[1] FALSE
D12V5, binary
                               cls
clus                              0   1
  AMP PEAK 12(9Q33.3) MUTATED     4  54
  AMP PEAK 12(9Q33.3) WILD-TYPE  10 414
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9Q33.3) MUTATED      4   54
  AMP PEAK 12(9Q33.3) WILD-TYPE   10  414
                                        clus
vv                                       AMP PEAK 12(9Q33.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             54
                                        clus
vv                                       AMP PEAK 12(9Q33.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              414
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(9Q33.3) MUTATED    26  29   1   1
  AMP PEAK 12(9Q33.3) WILD-TYPE 284 109   4  14
D12V6, multiclass
    clus
vv   AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  R0                          26                           284
  R1                          29                           109
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    46   0
  AMP PEAK 13(11Q13.2) WILD-TYPE 427   8
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            46                            435 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                             0                              8 
$`AMP PEAK 13(11Q13.2) MUTATED`
TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 
       11.51        35.01        26.99        33.11        48.53        25.68 
TCGA-EJ-8472 TCGA-EJ-A46G TCGA-EJ-A8FS TCGA-FC-A4JI TCGA-G9-7523 TCGA-HC-7745 
       24.85        21.96         8.75        13.45        28.18        23.70 
TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-A76W TCGA-HI-7168 TCGA-J9-A8CL TCGA-J9-A8CM 
       22.42        15.88         7.00        78.61        13.32        15.22 
TCGA-KC-A7FA TCGA-KK-A6E8 TCGA-KK-A8I4 TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IK 
       19.66        58.19        67.99        69.27        26.43        51.39 
TCGA-V1-A8WV TCGA-V1-A9OH TCGA-VN-A88K TCGA-X4-A8KS TCGA-XJ-A9DX TCGA-YJ-A8SW 
       22.55        41.19        25.51        32.19        31.99         4.87 
TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WH 
       48.72        60.56        56.52        46.29        62.79        14.04 
TCGA-YL-A9WI TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       53.36         4.27        11.67        29.85        19.17         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       16.96        22.75        17.98        11.47 

$`AMP PEAK 13(11Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-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-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-5496 TCGA-EJ-5497 
       33.01         2.99        29.00        27.16        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-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
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        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28        24.39        23.90        38.37        25.87        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        77.16        76.41        38.10        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        4.54         4.31         4.77        28.41        15.42        22.36 
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        83.87        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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        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        23.93         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        65.26         2.93        36.36        37.35        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        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
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        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
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        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       10.62        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       63.48         2.73        67.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR 
       53.36        42.94        44.88        14.76        45.47         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        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        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ 
       36.95        47.15        51.81        32.19        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SC 
       49.02        51.45        71.77        62.14        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       71.34         8.98        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-A9L2 
       28.34         3.09        14.53        13.28        10.13        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9LY 
       36.43        22.59        20.28        12.43        19.04        12.16 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                          3.78                           0.72 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                         78.61                         165.17 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                         25.18                          27.12 
[1] "3.8 - 78.6 (25.2)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "7.6e+07"
D13V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 13(11Q13.2) MUTATED     5  38   3
  AMP PEAK 13(11Q13.2) WILD-TYPE 183 243   7
D13V3, multiclass
    clus
vv   AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  T2                            5                            183
  T3                           38                            243
  T4                            3                              7
[1] 3 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    23  19
  AMP PEAK 13(11Q13.2) WILD-TYPE 315  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.2) MUTATED     23   19
  AMP PEAK 13(11Q13.2) WILD-TYPE  315   56
   clus
vv  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  0                           23                            315
  1                           19                             56
[1] 2 2
[1] FALSE
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.2) MUTATED     2  44
  AMP PEAK 13(11Q13.2) WILD-TYPE  12 424
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.2) MUTATED      2   44
  AMP PEAK 13(11Q13.2) WILD-TYPE   12  424
                                        clus
vv                                       AMP PEAK 13(11Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              44
                                        clus
vv                                       AMP PEAK 13(11Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               424
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(11Q13.2) MUTATED    20  24   0   2
  AMP PEAK 13(11Q13.2) WILD-TYPE 290 114   5  13
D13V6, multiclass
    clus
vv   AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  R0                           20                            290
  R1                           24                            114
  R2                            0                              5
  RX                            2                             13
[1] 4 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    36   0
  AMP PEAK 14(12Q23.1) WILD-TYPE 437   8
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            36                            445 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                             0                              8 
$`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-EJ-A7NH TCGA-FC-A4JI TCGA-G9-7521 TCGA-HC-8264 
       38.76        18.41        15.58        13.45        30.97         1.58 
TCGA-HC-8265 TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KK-A7AZ TCGA-KK-A8I7 
       15.88        13.32        40.67        12.69        49.94        65.82 
TCGA-KK-A8ID TCGA-V1-A8MF TCGA-V1-A9OH TCGA-VP-A87H TCGA-XJ-A9DX TCGA-XK-AAIV 
       69.27        41.23        41.19        21.80        31.99        37.25 
TCGA-YL-A8S8 TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WY TCGA-ZG-A9L0 
       62.14       114.38        62.79        14.04        28.34        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9N3 
       29.85        20.28        19.17        19.04        12.16        11.47 

$`AMP PEAK 14(12Q23.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         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-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        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-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        60.23        46.55        47.80        52.27 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       51.88        68.35        43.07        36.66        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
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-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        23.34        12.92        13.71        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ 
        7.56        11.61        28.70         8.22        14.20         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        4.54         4.31         4.77        28.41        15.42        22.36 
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        83.87        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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        52.93        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        23.93         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        65.26         2.93        36.36        37.35        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        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8266 TCGA-HC-A48F 
        2.27        22.55        17.95        22.32         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        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BL 
       27.12        13.87         5.85        10.62        15.22        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 
       52.93        58.36        27.02        34.65        51.68        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OL 
       58.39        79.73         6.71        20.91        38.93        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        85.18        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        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        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       46.29        32.45        71.34         8.98        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       62.37        24.33        49.91         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LM 
       10.13         4.27        37.94        36.43        22.59        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND 
        3.78        16.96        22.75        17.98        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                          0.92                           0.72 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                        114.38                         165.17 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                        29.095                         26.430 
[1] "0.9 - 114.4 (29.1)" "0.7 - 165.2 (26.4)"
[1] "hr="     "7.7e+07"
D14V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 14(12Q23.1) MUTATED     4  31   1
  AMP PEAK 14(12Q23.1) WILD-TYPE 184 250   9
D14V3, multiclass
    clus
vv   AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  T2                            4                            184
  T3                           31                            250
  T4                            1                              9
[1] 3 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    16  14
  AMP PEAK 14(12Q23.1) WILD-TYPE 322  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q23.1) MUTATED     16   14
  AMP PEAK 14(12Q23.1) WILD-TYPE  322   61
   clus
vv  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  0                           16                            322
  1                           14                             61
[1] 2 2
[1] FALSE
D14V5, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q23.1) MUTATED     1  35
  AMP PEAK 14(12Q23.1) WILD-TYPE  13 433
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q23.1) MUTATED      1   35
  AMP PEAK 14(12Q23.1) WILD-TYPE   13  433
                                        clus
vv                                       AMP PEAK 14(12Q23.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              35
                                        clus
vv                                       AMP PEAK 14(12Q23.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               433
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(12Q23.1) MUTATED    13  22   1   0
  AMP PEAK 14(12Q23.1) WILD-TYPE 297 116   4  15
D14V6, multiclass
    clus
vv   AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  R0                           13                            297
  R1                           22                            116
  R2                            1                              4
  RX                            0                             15
[1] 4 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    24   1
  AMP PEAK 15(13Q12.11) WILD-TYPE 449   7
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             25                             456 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                              1                               7 
$`AMP PEAK 15(13Q12.11) MUTATED`
TCGA-CH-5751 TCGA-CH-5788 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8472 TCGA-EJ-A46G 
       35.01        26.99        25.68        18.15        24.85        21.96 
TCGA-EJ-A65M TCGA-FC-A4JI TCGA-G9-6329 TCGA-HC-7209 TCGA-J9-A52B TCGA-J9-A52E 
        7.56        13.45        41.62        14.47        13.87        10.62 
TCGA-J9-A8CL TCGA-KC-A7F6 TCGA-KK-A8ID TCGA-KK-A8II TCGA-V1-A9ZI TCGA-VP-A872 
       13.32         8.65        69.27       113.98         4.70       111.39 
TCGA-XJ-A9DX TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SF TCGA-ZG-A9KY TCGA-ZG-A9L5 
       31.99        71.77        60.56        45.14         4.27        29.85 
TCGA-ZG-A9N3 
       11.47 

$`AMP PEAK 15(13Q12.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        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-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
       15.06        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-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        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
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-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       15.42        22.36        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        83.87        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        58.45        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 
       64.18        50.73        52.93        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        23.93         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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       37.35        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CM 
       20.28        11.77        13.55        27.12         5.85        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48         2.73        67.43        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       49.87         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        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        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       42.08        48.03         9.04         2.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       51.45        48.72        62.14        16.83        56.52        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       13.28        10.13        11.67        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        13.48         4.34 

  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                           4.27                            0.72 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                         113.98                          165.17 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                         24.850                          27.055 
[1] "4.3 - 114.0 (24.9)" "0.7 - 165.2 (27.1)"
[1] "hr=" "2.5"
D15V2, continuous
                                 vv
clus                               T2  T3  T4
  AMP PEAK 15(13Q12.11) MUTATED     5  17   3
  AMP PEAK 15(13Q12.11) WILD-TYPE 183 264   7
D15V3, multiclass
    clus
vv   AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  T2                             5                             183
  T3                            17                             264
  T4                             3                               7
[1] 3 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    15   7
  AMP PEAK 15(13Q12.11) WILD-TYPE 323  68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(13Q12.11) MUTATED     15    7
  AMP PEAK 15(13Q12.11) WILD-TYPE  323   68
   clus
vv  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  0                            15                             323
  1                             7                              68
[1] 2 2
[1] FALSE
D15V5, binary
                                 cls
clus                                0   1
  AMP PEAK 15(13Q12.11) MUTATED     3  22
  AMP PEAK 15(13Q12.11) WILD-TYPE  11 446
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(13Q12.11) MUTATED      3   22
  AMP PEAK 15(13Q12.11) WILD-TYPE   11  446
                                        clus
vv                                       AMP PEAK 15(13Q12.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               22
                                        clus
vv                                       AMP PEAK 15(13Q12.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                446
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 15(13Q12.11) MUTATED    12  12   0   0
  AMP PEAK 15(13Q12.11) WILD-TYPE 298 126   5  15
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  R0                            12                             298
  R1                            12                             126
  R2                             0                               5
  RX                             0                              15
[1] 4 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    26   1
  AMP PEAK 16(14Q21.1) WILD-TYPE 447   7
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            27                            454 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                             1                              7 
$`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        24.39 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-A9S0 TCGA-HC-8261 
       21.96        14.83        13.45         3.32        26.01        17.95 
TCGA-HC-8265 TCGA-HC-A631 TCGA-J4-AATZ TCGA-KC-A7FA TCGA-KK-A59Z TCGA-KK-A8I4 
       15.88         1.78        13.55        19.66        86.40        67.99 
TCGA-VP-A872 TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-YL-A8SK 
      111.39        42.08        31.99        37.25        41.49        46.29 
TCGA-ZG-A9L0 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       11.67        19.17         3.78 

$`AMP PEAK 16(14Q21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5753 TCGA-CH-5754 
       24.03         1.02        13.02        35.01         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-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        13.02        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 
       33.01         2.99        29.00        27.16        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-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-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        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        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       25.18        21.60        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6373 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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        32.68        23.93         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        65.26         2.93        36.36        37.35        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        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
        2.27        22.55        22.32         1.58         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        14.37        20.28        11.77        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55         6.64        58.39        79.73         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.81        41.42        44.91        25.78        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        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        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI 
       45.47        32.19         3.91        37.05        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        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        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        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        45.86        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        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         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
        4.27        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       12.43        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                          0.92                           0.72 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                        111.39                         165.17 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                        21.960                         27.055 
[1] "0.9 - 111.4 (22.0)" "0.7 - 165.2 (27.1)"
[1] "hr=" "4.1"
D16V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 16(14Q21.1) MUTATED     6  21   0
  AMP PEAK 16(14Q21.1) WILD-TYPE 182 260  10
D16V3, multiclass
    clus
vv   AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  T2                            6                            182
  T3                           21                            260
  T4                            0                             10
[1] 3 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    15   8
  AMP PEAK 16(14Q21.1) WILD-TYPE 323  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(14Q21.1) MUTATED     15    8
  AMP PEAK 16(14Q21.1) WILD-TYPE  323   67
   clus
vv  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  0                           15                            323
  1                            8                             67
[1] 2 2
[1] FALSE
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(14Q21.1) MUTATED     2  25
  AMP PEAK 16(14Q21.1) WILD-TYPE  12 443
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(14Q21.1) MUTATED      2   25
  AMP PEAK 16(14Q21.1) WILD-TYPE   12  443
                                        clus
vv                                       AMP PEAK 16(14Q21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              25
                                        clus
vv                                       AMP PEAK 16(14Q21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               443
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(14Q21.1) MUTATED    16  11   0   0
  AMP PEAK 16(14Q21.1) WILD-TYPE 294 127   5  15
D16V6, multiclass
    clus
vv   AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  R0                           16                            294
  R1                           11                            127
  R2                            0                              5
  RX                            0                             15
[1] 4 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    14   1
  AMP PEAK 17(15Q11.2) WILD-TYPE 459   7
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                            15                            466 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                             1                              7 
$`AMP PEAK 17(15Q11.2) MUTATED`
TCGA-EJ-5514 TCGA-EJ-7328 TCGA-EJ-8472 TCGA-G9-7525 TCGA-HC-A6AO TCGA-HC-A76W 
       36.23        27.68        24.85        32.68        17.42         7.00 
TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A8ID TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YL-A8SK 
        6.44        58.36        69.27        31.99        37.25        46.29 
TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-ZG-A9KY 
       14.04        60.99         4.27 

$`AMP PEAK 17(15Q11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        35.18        30.35         6.28        24.39        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 
       77.16        76.41        38.10        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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        58.45        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 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        28.18        26.01        23.93         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        65.26         2.93        36.36        37.35 
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        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        4.41         4.93         9.53        25.48        18.84        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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       13.55        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        67.07        58.19        52.93        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48         2.73        67.43        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        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        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        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        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        45.86        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        53.36        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                          4.27                           0.72 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                         69.27                         165.17 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                        31.990                         26.365 
[1] "4.3 - 69.3 (32.0)"  "0.7 - 165.2 (26.4)"
[1] "hr=" "5.4"
D17V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 17(15Q11.2) MUTATED     3  11   1
  AMP PEAK 17(15Q11.2) WILD-TYPE 185 270   9
D17V3, multiclass
    clus
vv   AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  T2                            3                            185
  T3                           11                            270
  T4                            1                              9
[1] 3 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     5   9
  AMP PEAK 17(15Q11.2) WILD-TYPE 333  66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q11.2) MUTATED      5    9
  AMP PEAK 17(15Q11.2) WILD-TYPE  333   66
   clus
vv  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  0                            5                            333
  1                            9                             66
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q11.2) MUTATED     0  15
  AMP PEAK 17(15Q11.2) WILD-TYPE  14 453
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q11.2) MUTATED      0   15
  AMP PEAK 17(15Q11.2) WILD-TYPE   14  453
                                        clus
vv                                       AMP PEAK 17(15Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              15
                                        clus
vv                                       AMP PEAK 17(15Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               453
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(15Q11.2) MUTATED     5  10   0   0
  AMP PEAK 17(15Q11.2) WILD-TYPE 305 128   5  15
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  R0                            5                            305
  R1                           10                            128
  R2                            0                              5
  RX                            0                             15
[1] 4 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    29   0
  AMP PEAK 18(16Q11.2) WILD-TYPE 444   8
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            29                            452 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                             0                              8 
$`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        76.41 
TCGA-FC-A4JI TCGA-HC-7210 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-A4ZV TCGA-HC-A8CY 
       13.45        28.54        38.17         1.48         0.76         9.53 
TCGA-HI-7168 TCGA-KK-A7AP TCGA-KK-A7B4 TCGA-KK-A8I7 TCGA-KK-A8ID TCGA-KK-A8IF 
       78.61         6.44        20.94        65.82        69.27        26.43 
TCGA-QU-A6IL TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9ZI TCGA-VP-A87K TCGA-XJ-A9DX 
        3.19        79.73        20.91         4.70        42.94        31.99 
TCGA-YJ-A8SW TCGA-YL-A8S9 TCGA-YL-A9WH TCGA-ZG-A9LZ TCGA-ZG-A9NI 
        4.87        60.56        14.04        22.75         4.34 

$`AMP PEAK 18(16Q11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        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-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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 
       30.35         6.28        24.39        23.90        38.37        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-8470 TCGA-EJ-8472 
        3.75        23.05        19.92        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42        22.36        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        83.87 
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        58.45        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        64.18        50.73        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 
        2.93        36.36        37.35        14.47         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       40.08         1.68         2.37        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       31.69        23.57         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        4.41         7.00         4.93        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       67.99       101.79        21.96        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
        2.73        67.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
        6.64        58.39         6.71        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       17.75        49.87         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       38.04        42.08        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 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       47.15        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        71.77        62.14        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI 
       32.45       114.38        71.34        62.79         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                          0.76                           0.72 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                         79.73                         165.17 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                        22.750                         27.055 
[1] "0.8 - 79.7 (22.8)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "2.7e+07"
D18V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 18(16Q11.2) MUTATED     2  26   1
  AMP PEAK 18(16Q11.2) WILD-TYPE 186 255   9
D18V3, multiclass
    clus
vv   AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  T2                            2                            186
  T3                           26                            255
  T4                            1                              9
[1] 3 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    19   8
  AMP PEAK 18(16Q11.2) WILD-TYPE 319  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16Q11.2) MUTATED     19    8
  AMP PEAK 18(16Q11.2) WILD-TYPE  319   67
   clus
vv  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  0                           19                            319
  1                            8                             67
[1] 2 2
[1] FALSE
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(16Q11.2) MUTATED     2  27
  AMP PEAK 18(16Q11.2) WILD-TYPE  12 441
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16Q11.2) MUTATED      2   27
  AMP PEAK 18(16Q11.2) WILD-TYPE   12  441
                                        clus
vv                                       AMP PEAK 18(16Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              27
                                        clus
vv                                       AMP PEAK 18(16Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               441
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(16Q11.2) MUTATED    13  15   0   1
  AMP PEAK 18(16Q11.2) WILD-TYPE 297 123   5  14
D18V6, multiclass
    clus
vv   AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  R0                           13                            297
  R1                           15                            123
  R2                            0                              5
  RX                            1                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    24   0
  AMP PEAK 19(17Q23.2) WILD-TYPE 449   8
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            24                            457 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                             0                              8 
$`AMP PEAK 19(17Q23.2) MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5527 TCGA-EJ-7781 
       32.71        11.51        23.90        36.23        39.75        23.90 
TCGA-EJ-A46G TCGA-EJ-A65F TCGA-HC-7745 TCGA-HC-8216 TCGA-HI-7168 TCGA-J4-A67L 
       21.96        18.41        23.70        22.42        78.61        25.32 
TCGA-J9-A8CL TCGA-KK-A7AP TCGA-KK-A8I6 TCGA-KK-A8ID TCGA-TP-A8TT TCGA-XK-AAIV 
       13.32         6.44        21.96        69.27        11.90        37.25 
TCGA-YJ-A8SW TCGA-YL-A9WH TCGA-ZG-A9KY TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9NI 
        4.87        14.04         4.27        12.16        17.98         4.34 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         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-5508 TCGA-EJ-5509 
       45.73        28.93        30.31        27.19        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-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       38.76        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        24.39        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       25.18        21.60        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        23.34        12.92        13.71        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        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        83.87        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        58.45        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        64.18        50.73        52.93        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        23.93 
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        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        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 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        2.10        31.69        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        31.43        19.36        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        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 
       33.01        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM 
       13.55        27.12        13.87         5.85        10.62        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94        67.99       101.79        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        67.43        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
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        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       47.15        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        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 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        16.96        19.04        22.75        14.96        11.47 
TCGA-ZG-A9ND 
       13.48 

  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                          4.27                           0.72 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                         78.61                         165.17 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                         21.96                          27.19 
[1] "4.3 - 78.6 (22.0)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9400000"
D19V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 19(17Q23.2) MUTATED     2  20   2
  AMP PEAK 19(17Q23.2) WILD-TYPE 186 261   8
D19V3, multiclass
    clus
vv   AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  T2                            2                            186
  T3                           20                            261
  T4                            2                              8
[1] 3 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    14   9
  AMP PEAK 19(17Q23.2) WILD-TYPE 324  66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q23.2) MUTATED     14    9
  AMP PEAK 19(17Q23.2) WILD-TYPE  324   66
   clus
vv  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  0                           14                            324
  1                            9                             66
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q23.2) MUTATED     3  21
  AMP PEAK 19(17Q23.2) WILD-TYPE  11 447
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q23.2) MUTATED      3   21
  AMP PEAK 19(17Q23.2) WILD-TYPE   11  447
                                        clus
vv                                       AMP PEAK 19(17Q23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              21
                                        clus
vv                                       AMP PEAK 19(17Q23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               447
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(17Q23.2) MUTATED    12  12   0   0
  AMP PEAK 19(17Q23.2) WILD-TYPE 298 126   5  15
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  R0                           12                            298
  R1                           12                            126
  R2                            0                              5
  RX                            0                             15
[1] 4 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    17   0
  AMP PEAK 20(19Q13.43) WILD-TYPE 456   8
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             17                             464 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                              0                               8 
$`AMP PEAK 20(19Q13.43) MUTATED`
TCGA-EJ-5518 TCGA-EJ-A46G TCGA-HC-7078 TCGA-HC-7213 TCGA-HI-7168 TCGA-KK-A7B4 
       52.27        21.96        65.26        40.08        78.61        20.94 
TCGA-KK-A8ID TCGA-V1-A8WV TCGA-VP-A875 TCGA-VP-A87D TCGA-XK-AAIV TCGA-YJ-A8SW 
       69.27        22.55        75.91        60.92        37.25         4.87 
TCGA-YL-A8HO TCGA-YL-A8SB TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9N3 
       71.77        56.52        19.17        12.43        11.47 

$`AMP PEAK 20(19Q13.43) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5519 TCGA-EJ-5521 
       36.23        60.23        46.55        47.80        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
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-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       21.60        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        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        83.87        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        58.45        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        64.18        50.73        52.93        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        23.93 
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        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       37.35        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        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78        16.31       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        85.18        55.56        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ 
       36.95        47.15        51.81        32.19        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        62.14        60.56        16.83 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN 
       37.94        36.43        29.85        22.59        20.28         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                           4.87                            0.72 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                          78.61                          165.17 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                         40.080                          26.365 
[1] "4.9 - 78.6 (40.1)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "2.7e+07"
D20V2, continuous
                                 vv
clus                               T2  T3  T4
  AMP PEAK 20(19Q13.43) MUTATED     0  16   1
  AMP PEAK 20(19Q13.43) WILD-TYPE 188 265   9
D20V3, multiclass
    clus
vv   AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  T2                             0                             188
  T3                            16                             265
  T4                             1                               9
[1] 3 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    10   7
  AMP PEAK 20(19Q13.43) WILD-TYPE 328  68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.43) MUTATED     10    7
  AMP PEAK 20(19Q13.43) WILD-TYPE  328   68
   clus
vv  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  0                            10                             328
  1                             7                              68
[1] 2 2
[1] FALSE
D20V5, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.43) MUTATED     2  15
  AMP PEAK 20(19Q13.43) WILD-TYPE  12 453
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.43) MUTATED      2   15
  AMP PEAK 20(19Q13.43) WILD-TYPE   12  453
                                        clus
vv                                       AMP PEAK 20(19Q13.43) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               15
                                        clus
vv                                       AMP PEAK 20(19Q13.43) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                453
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(19Q13.43) MUTATED     8   9   0   0
  AMP PEAK 20(19Q13.43) WILD-TYPE 302 129   5  15
D20V6, multiclass
    clus
vv   AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  R0                             8                             302
  R1                             9                             129
  R2                             0                               5
  RX                             0                              15
[1] 4 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    42   0
  AMP PEAK 21(20Q13.2) WILD-TYPE 431   8
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            42                            439 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                             0                              8 
$`AMP PEAK 21(20Q13.2) MUTATED`
TCGA-4L-AA1F TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5772 TCGA-EJ-5518 TCGA-EJ-5532 
       11.51         0.92        44.02        15.98        52.27        47.87 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-8472 TCGA-EJ-A65M TCGA-G9-6494 TCGA-G9-6499 
       37.81        33.14        24.85         7.56        58.22        50.73 
TCGA-HC-8265 TCGA-HI-7168 TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KK-A6E8 
       15.88        78.61        10.62        13.32        40.67        58.19 
TCGA-KK-A8I4 TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IK TCGA-V1-A9O5 TCGA-V1-A9OL 
       67.99        69.27        26.43        51.39        58.39        19.36 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIV 
      111.39        75.91        60.92        42.08        31.99        37.25 
TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A8QY 
        4.87        48.72        62.14        14.04        53.36        13.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       12.43         3.78        19.04        22.75        17.98        11.47 

$`AMP PEAK 21(20Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        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-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
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-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        41.85        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       93.70        83.57        36.13        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        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 
       77.16        76.41        38.10        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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        83.87        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-G9-7509 
       58.45        25.15        27.29        56.75        64.18        52.93 
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        23.93         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 
       65.26         2.93        36.36        37.35        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        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
       22.55        17.95        22.32         1.58         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        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        4.93         9.53        25.48        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.87         5.85        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        29.56        20.94       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IG 
       31.79        32.91        63.48         2.73        67.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58        22.55         6.64        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        41.19        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.81        41.42        44.91        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
       97.41        23.93        85.18        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
        3.91        37.05        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        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       47.15        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       51.45        71.77        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK 
      114.38        71.34        62.79         8.98        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
       24.33        49.91        28.34         3.09        14.53        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
       20.28        19.17        16.96        12.16        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                          0.92                           0.72 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                        111.39                         165.17 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                        35.195                         26.040 
[1] "0.9 - 111.4 (35.2)" "0.7 - 165.2 (26.0)"
[1] "hr="     "7.9e+07"
D21V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 21(20Q13.2) MUTATED     4  35   3
  AMP PEAK 21(20Q13.2) WILD-TYPE 184 246   7
D21V3, multiclass
    clus
vv   AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  T2                            4                            184
  T3                           35                            246
  T4                            3                              7
[1] 3 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    26  13
  AMP PEAK 21(20Q13.2) WILD-TYPE 312  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20Q13.2) MUTATED     26   13
  AMP PEAK 21(20Q13.2) WILD-TYPE  312   62
   clus
vv  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  0                           26                            312
  1                           13                             62
[1] 2 2
[1] FALSE
D21V5, binary
                                cls
clus                               0   1
  AMP PEAK 21(20Q13.2) MUTATED     2  40
  AMP PEAK 21(20Q13.2) WILD-TYPE  12 428
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20Q13.2) MUTATED      2   40
  AMP PEAK 21(20Q13.2) WILD-TYPE   12  428
                                        clus
vv                                       AMP PEAK 21(20Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              40
                                        clus
vv                                       AMP PEAK 21(20Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               428
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(20Q13.2) MUTATED    18  21   0   2
  AMP PEAK 21(20Q13.2) WILD-TYPE 292 117   5  13
D21V6, multiclass
    clus
vv   AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  R0                           18                            292
  R1                           21                            117
  R2                            0                              5
  RX                            2                             13
[1] 4 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    24   0
  AMP PEAK 22(XP22.11) WILD-TYPE 449   8
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            24                            457 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                             0                              8 
$`AMP PEAK 22(XP22.11) MUTATED`
TCGA-4L-AA1F TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65D TCGA-HC-7742 TCGA-HC-7747 
       11.51        18.15        21.96        12.92         1.48        24.59 
TCGA-HC-7818 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-HC-A8CY TCGA-J9-A8CM 
       30.84        31.43        22.42         0.76         9.53        15.22 
TCGA-KK-A6E8 TCGA-TP-A8TT TCGA-V1-A9O5 TCGA-VN-A943 TCGA-VP-A87H TCGA-XK-AAJA 
       58.19        11.90        58.39        16.31        21.80        30.58 
TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK TCGA-ZG-A9KY TCGA-ZG-A9L5 
        4.87        62.14        41.46        46.29         4.27        29.85 

$`AMP PEAK 22(XP22.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
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-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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        83.87        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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        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        23.93         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        65.26         2.93        36.36        37.35 
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        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
       23.57         1.68        23.70        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 
       25.71        30.51        17.85        24.56        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15        22.36         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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TV 
       41.00       140.19       122.17        86.14        18.12        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       85.18        55.56        60.92        66.97        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        37.25        40.04        41.49        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       47.15        51.81        32.19        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        71.77        60.56        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       13.28        10.13        11.67        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                          0.76                           0.72 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                         62.14                         165.17 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                         21.88                          27.09 
[1] "0.8 - 62.1 (21.9)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "2.6e+07"
D22V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 22(XP22.11) MUTATED     4  17   3
  AMP PEAK 22(XP22.11) WILD-TYPE 184 264   7
D22V3, multiclass
    clus
vv   AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  T2                            4                            184
  T3                           17                            264
  T4                            3                              7
[1] 3 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    17   7
  AMP PEAK 22(XP22.11) WILD-TYPE 321  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(XP22.11) MUTATED     17    7
  AMP PEAK 22(XP22.11) WILD-TYPE  321   68
   clus
vv  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  0                           17                            321
  1                            7                             68
[1] 2 2
[1] FALSE
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(XP22.11) MUTATED     3  21
  AMP PEAK 22(XP22.11) WILD-TYPE  11 447
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(XP22.11) MUTATED      3   21
  AMP PEAK 22(XP22.11) WILD-TYPE   11  447
                                        clus
vv                                       AMP PEAK 22(XP22.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              21
                                        clus
vv                                       AMP PEAK 22(XP22.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               447
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(XP22.11) MUTATED     9  11   1   1
  AMP PEAK 22(XP22.11) WILD-TYPE 301 127   4  14
D22V6, multiclass
    clus
vv   AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  R0                            9                            301
  R1                           11                            127
  R2                            1                              4
  RX                            1                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    23   0
  AMP PEAK 23(XP22.11) WILD-TYPE 450   8
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            23                            458 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                             0                              8 
$`AMP PEAK 23(XP22.11) MUTATED`
TCGA-4L-AA1F TCGA-EJ-5502 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-7789 TCGA-EJ-A46G 
       11.51        26.30        46.55        47.80        18.15        21.96 
TCGA-EJ-A65D TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-HC-A8CY TCGA-J9-A8CM 
       12.92        31.43        22.42         0.76         9.53        15.22 
TCGA-KK-A6E8 TCGA-V1-A9O5 TCGA-VN-A943 TCGA-VP-A87H TCGA-XK-AAJA TCGA-YJ-A8SW 
       58.19        58.39        16.31        21.80        30.58         4.87 
TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK TCGA-ZG-A9KY TCGA-ZG-A9L5 
       62.14        41.46        46.29         4.27        29.85 

$`AMP PEAK 23(XP22.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-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-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 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        23.34        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        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        83.87 
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        58.45        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        64.18        50.73        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 
       30.51        30.84        17.85        24.56        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15        22.36         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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93        25.48        18.84 
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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        85.18        55.56        60.92        66.97        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        41.49        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ 
       36.95        47.15        51.81        32.19        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       56.52        45.14        28.77        53.06        45.86        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                          0.76                           0.72 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                         62.14                         165.17 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                        22.420                         27.005 
[1] "0.8 - 62.1 (22.4)"  "0.7 - 165.2 (27.0)"
[1] "hr="     "2.6e+07"
D23V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 23(XP22.11) MUTATED     4  16   3
  AMP PEAK 23(XP22.11) WILD-TYPE 184 265   7
D23V3, multiclass
    clus
vv   AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  T2                            4                            184
  T3                           16                            265
  T4                            3                              7
[1] 3 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    16   7
  AMP PEAK 23(XP22.11) WILD-TYPE 322  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(XP22.11) MUTATED     16    7
  AMP PEAK 23(XP22.11) WILD-TYPE  322   68
   clus
vv  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  0                           16                            322
  1                            7                             68
[1] 2 2
[1] FALSE
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(XP22.11) MUTATED     3  20
  AMP PEAK 23(XP22.11) WILD-TYPE  11 448
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(XP22.11) MUTATED      3   20
  AMP PEAK 23(XP22.11) WILD-TYPE   11  448
                                        clus
vv                                       AMP PEAK 23(XP22.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              20
                                        clus
vv                                       AMP PEAK 23(XP22.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               448
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(XP22.11) MUTATED     9  11   1   1
  AMP PEAK 23(XP22.11) WILD-TYPE 301 127   4  14
D23V6, multiclass
    clus
vv   AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  R0                            9                            301
  R1                           11                            127
  R2                            1                              4
  RX                            1                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    22   0
  AMP PEAK 24(XP21.1) WILD-TYPE 451   8
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           22                           459 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                            0                             8 
$`AMP PEAK 24(XP21.1) MUTATED`
TCGA-4L-AA1F TCGA-EJ-5495 TCGA-EJ-5499 TCGA-EJ-5530 TCGA-EJ-7789 TCGA-EJ-A46G 
       11.51        33.11        46.52        60.23        18.15        21.96 
TCGA-EJ-A65D TCGA-HC-8216 TCGA-HC-A4ZV TCGA-J9-A8CM TCGA-KK-A6E8 TCGA-KK-A8ID 
       12.92        22.42         0.76        15.22        58.19        69.27 
TCGA-V1-A9O5 TCGA-VN-A943 TCGA-VP-A87H TCGA-XJ-A9DX TCGA-XK-AAJA TCGA-YJ-A8SW 
       58.39        16.31        21.80        31.99        30.58         4.87 
TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK TCGA-ZG-A9L5 
       62.14        41.46        46.29        29.85 

$`AMP PEAK 24(XP21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       19.56        13.32        29.79        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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        39.75        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        23.34        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        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        83.87 
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        58.45        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        64.18        50.73        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 
       22.32         1.58        15.88         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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        13.32        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ 
      115.13        49.25       113.33        67.07         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       67.43        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       22.55         6.64        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        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        37.25        40.04        41.49        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ 
       36.95        47.15        51.81        32.19        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       56.52        45.14        28.77        53.06        45.86        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                         0.76                          0.72 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                        69.27                        165.17 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                       30.215                        26.430 
[1] "0.8 - 69.3 (30.2)"  "0.7 - 165.2 (26.4)"
[1] "hr="     "2.6e+07"
D24V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 24(XP21.1) MUTATED     3  17   2
  AMP PEAK 24(XP21.1) WILD-TYPE 185 264   8
D24V3, multiclass
    clus
vv   AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  T2                           3                           185
  T3                          17                           264
  T4                           2                             8
[1] 3 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    15   7
  AMP PEAK 24(XP21.1) WILD-TYPE 323  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.1) MUTATED     15    7
  AMP PEAK 24(XP21.1) WILD-TYPE  323   68
   clus
vv  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  0                          15                           323
  1                           7                            68
[1] 2 2
[1] FALSE
D24V5, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.1) MUTATED     3  19
  AMP PEAK 24(XP21.1) WILD-TYPE  11 449
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.1) MUTATED      3   19
  AMP PEAK 24(XP21.1) WILD-TYPE   11  449
                                        clus
vv                                       AMP PEAK 24(XP21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             19
                                        clus
vv                                       AMP PEAK 24(XP21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              449
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 24(XP21.1) MUTATED     9  11   1   1
  AMP PEAK 24(XP21.1) WILD-TYPE 301 127   4  14
D24V6, multiclass
    clus
vv   AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  R0                           9                           301
  R1                          11                           127
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    15   0
  AMP PEAK 25(XQ21.1) WILD-TYPE 458   8
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           15                           466 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                            0                             8 
$`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-V1-A9O5 TCGA-VN-A943 TCGA-VP-A87H TCGA-YL-A8S8 
       50.73        58.19        58.39        16.31        21.80        62.14 
TCGA-YL-A8SC TCGA-YL-A9WI TCGA-ZG-A9L5 
       41.46        53.36        29.85 

$`AMP PEAK 25(XQ21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5506 TCGA-EJ-5508 
       44.88        26.30        45.73        28.93        27.19        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-5522 TCGA-EJ-5524 
       46.55        47.80        52.27        64.50        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       36.66        38.76        39.75        41.85        47.87        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        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 
       83.87        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        58.45        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        64.18        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
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        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       85.18        55.56        60.92        66.97        53.36        42.94 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        37.25        40.04        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        56.52        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
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-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        36.43        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        16.31                          0.72 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        62.14                        165.17 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                       41.460                        26.025 
[1] "16.3 - 62.1 (41.5)" "0.7 - 165.2 (26.0)"
[1] "hr="     "2.6e+07"
D25V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 25(XQ21.1) MUTATED     4   9   2
  AMP PEAK 25(XQ21.1) WILD-TYPE 184 272   8
D25V3, multiclass
    clus
vv   AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  T2                           4                           184
  T3                           9                           272
  T4                           2                             8
[1] 3 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   4
  AMP PEAK 25(XQ21.1) WILD-TYPE 327  71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED     11    4
  AMP PEAK 25(XQ21.1) WILD-TYPE  327   71
   clus
vv  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  0                          11                           327
  1                           4                            71
[1] 2 2
[1] FALSE
D25V5, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED     0  15
  AMP PEAK 25(XQ21.1) WILD-TYPE  14 453
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED      0   15
  AMP PEAK 25(XQ21.1) WILD-TYPE   14  453
                                        clus
vv                                       AMP PEAK 25(XQ21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             15
                                        clus
vv                                       AMP PEAK 25(XQ21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              453
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 25(XQ21.1) MUTATED     9   4   1   1
  AMP PEAK 25(XQ21.1) WILD-TYPE 301 134   4  14
D25V6, multiclass
    clus
vv   AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  R0                           9                           301
  R1                           4                           134
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    13   0
  AMP PEAK 26(XQ21.1) WILD-TYPE 460   8
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           13                           468 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                            0                             8 
$`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-V1-A9O5 TCGA-VN-A943 TCGA-VP-A87H TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A9WI 
       58.39        16.31        21.80        62.14        41.46        53.36 
TCGA-ZG-A9L5 
       29.85 

$`AMP PEAK 26(XQ21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5521 
       36.23        60.23        46.55        47.80        52.27        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        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        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        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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        58.45        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 
       64.18        52.93        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        23.93         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        65.26         2.93        36.36        37.35 
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        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 TCGA-HC-7740 
        2.37        38.17        44.55         0.72        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        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        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
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 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       22.55         6.64        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       53.36        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        31.99        31.96        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH 
       71.77        60.56        16.83        56.52        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79         8.98        14.04        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         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
        4.27        11.67        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                         2.10                          0.72 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                        64.50                        165.17 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                        41.85                         26.17 
[1] "2.1 - 64.5 (41.9)"  "0.7 - 165.2 (26.2)"
[1] "hr="     "2.6e+07"
D26V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 26(XQ21.1) MUTATED     3   8   2
  AMP PEAK 26(XQ21.1) WILD-TYPE 185 273   8
D26V3, multiclass
    clus
vv   AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  T2                           3                           185
  T3                           8                           273
  T4                           2                             8
[1] 3 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   5
  AMP PEAK 26(XQ21.1) WILD-TYPE 330  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(XQ21.1) MUTATED      8    5
  AMP PEAK 26(XQ21.1) WILD-TYPE  330   70
   clus
vv  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  0                           8                           330
  1                           5                            70
[1] 2 2
[1] FALSE
D26V5, binary
                               cls
clus                              0   1
  AMP PEAK 26(XQ21.1) MUTATED     0  13
  AMP PEAK 26(XQ21.1) WILD-TYPE  14 455
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(XQ21.1) MUTATED      0   13
  AMP PEAK 26(XQ21.1) WILD-TYPE   14  455
                                        clus
vv                                       AMP PEAK 26(XQ21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             13
                                        clus
vv                                       AMP PEAK 26(XQ21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              455
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 26(XQ21.1) MUTATED     7   4   1   1
  AMP PEAK 26(XQ21.1) WILD-TYPE 303 134   4  14
D26V6, multiclass
    clus
vv   AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  R0                           7                           303
  R1                           4                           134
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    17   0
  AMP PEAK 27(XQ25) WILD-TYPE 456   8
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         17                         464 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                          0                           8 
$`AMP PEAK 27(XQ25) MUTATED`
TCGA-EJ-5499 TCGA-EJ-5505 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7789 TCGA-EJ-A8FN 
       46.52        30.31        68.35        38.76        18.15        10.82 
TCGA-G9-6499 TCGA-KK-A6E8 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-VN-A943 TCGA-VP-A87H 
       50.73        58.19        58.39         6.71        16.31        21.80 
TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A9WI TCGA-ZG-A9L5 
       30.58        62.14        41.46        53.36        29.85 

$`AMP PEAK 27(XQ25) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 
       27.16        33.11        19.56        13.32        29.79        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       26.30        45.73        28.93        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-5524 
       46.55        47.80        52.27        64.50        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-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        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 
       83.87        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        58.45        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        64.18        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
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        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       25.08        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
      140.19       122.17        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       79.73        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       49.87         4.70         5.82         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        41.49        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        71.77        60.56        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ 
      114.38        71.34        62.79         8.98        14.04        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                       6.71                        0.72 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                      68.35                      165.17 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                     38.760                      26.025 
[1] "6.7 - 68.3 (38.8)"  "0.7 - 165.2 (26.0)"
[1] "hr="     "2.6e+07"
D27V2, continuous
                             vv
clus                           T2  T3  T4
  AMP PEAK 27(XQ25) MUTATED     5  10   2
  AMP PEAK 27(XQ25) WILD-TYPE 183 271   8
D27V3, multiclass
    clus
vv   AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  T2                         5                         183
  T3                        10                         271
  T4                         2                           8
[1] 3 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    13   4
  AMP PEAK 27(XQ25) WILD-TYPE 325  71
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ25) MUTATED     13    4
  AMP PEAK 27(XQ25) WILD-TYPE  325   71
   clus
vv  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  0                        13                         325
  1                         4                          71
[1] 2 2
[1] FALSE
D27V5, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ25) MUTATED     0  17
  AMP PEAK 27(XQ25) WILD-TYPE  14 451
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ25) MUTATED      0   17
  AMP PEAK 27(XQ25) WILD-TYPE   14  451
                                        clus
vv                                       AMP PEAK 27(XQ25) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           17
                                        clus
vv                                       AMP PEAK 27(XQ25) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            451
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 27(XQ25) MUTATED    11   4   1   1
  AMP PEAK 27(XQ25) WILD-TYPE 299 134   4  14
D27V6, multiclass
    clus
vv   AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  R0                        11                         299
  R1                         4                         134
  R2                         1                           4
  RX                         1                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    17   0
  AMP PEAK 28(XQ27.1) WILD-TYPE 456   8
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           17                           464 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                            0                             8 
$`AMP PEAK 28(XQ27.1) MUTATED`
TCGA-EJ-7331 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-G9-6499 
       24.39        25.87        18.15        17.29        23.05        50.73 
TCGA-H9-7775 TCGA-HC-7744 TCGA-HC-7749 TCGA-KK-A6E8 TCGA-V1-A9O5 TCGA-V1-A9O9 
        6.08         1.68         1.97        58.19        58.39         6.71 
TCGA-VN-A943 TCGA-VP-A87H TCGA-YL-A8S8 TCGA-YL-A9WI TCGA-ZG-A9L5 
       16.31        21.80        62.14        53.36        29.85 

$`AMP PEAK 28(XQ27.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-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        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
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-7791 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
       19.59         3.75        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        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        83.87        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        58.45 
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        64.18        52.93 
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-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       26.01        23.93        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 
        0.72         2.10        31.69        23.57         1.48        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        26.04        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP 
       67.59       115.13        49.25       113.33        67.07         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OA 
       30.38        15.58        22.55         6.64        79.73        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       41.49        30.58        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.19        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        71.77        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ 
      114.38        71.34        62.79         8.98        14.04        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                         1.68                          0.72 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                        62.14                        165.17 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                       23.050                        27.055 
[1] "1.7 - 62.1 (23.1)"  "0.7 - 165.2 (27.1)"
[1] "hr="     "9300000"
D28V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 28(XQ27.1) MUTATED     6   9   2
  AMP PEAK 28(XQ27.1) WILD-TYPE 182 272   8
D28V3, multiclass
    clus
vv   AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  T2                           6                           182
  T3                           9                           272
  T4                           2                             8
[1] 3 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    13   3
  AMP PEAK 28(XQ27.1) WILD-TYPE 325  72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 28(XQ27.1) MUTATED     13    3
  AMP PEAK 28(XQ27.1) WILD-TYPE  325   72
   clus
vv  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  0                          13                           325
  1                           3                            72
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                              0   1
  AMP PEAK 28(XQ27.1) MUTATED     0  17
  AMP PEAK 28(XQ27.1) WILD-TYPE  14 451
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 28(XQ27.1) MUTATED      0   17
  AMP PEAK 28(XQ27.1) WILD-TYPE   14  451
                                        clus
vv                                       AMP PEAK 28(XQ27.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             17
                                        clus
vv                                       AMP PEAK 28(XQ27.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              451
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 28(XQ27.1) MUTATED    10   4   1   1
  AMP PEAK 28(XQ27.1) WILD-TYPE 300 134   4  14
D28V6, multiclass
    clus
vv   AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  R0                          10                           300
  R1                           4                           134
  R2                           1                             4
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    55   2
  DEL PEAK  1(1P31.3) WILD-TYPE 418   6
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           57                           424 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                            2                             6 
$`DEL PEAK  1(1P31.3) MUTATED`
TCGA-2A-AAYU TCGA-CH-5740 TCGA-CH-5753 TCGA-CH-5769 TCGA-CH-5791 TCGA-CH-5794 
       20.22         1.02         1.02         2.04        33.01        29.00 
TCGA-EJ-5499 TCGA-EJ-5504 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8472 TCGA-FC-7961 
       46.52        28.93        25.68        14.14        24.85        15.42 
TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6379 TCGA-G9-6499 
       87.35        55.76        46.16        46.52        58.45        50.73 
TCGA-G9-7525 TCGA-HC-7078 TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-A48F 
       32.68        65.26        37.35        40.08         2.37        22.36 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52E TCGA-J9-A8CL 
        0.76         2.01        78.61        43.69        10.62        13.32 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A8IA 
       86.40        30.02        54.54       115.13       113.33        63.48 
TCGA-KK-A8IG TCGA-KK-A8IK TCGA-M7-A725 TCGA-QU-A6IL TCGA-V1-A8WV TCGA-V1-A9O7 
       82.36        51.39        18.84         3.19        22.55        79.73 
TCGA-V1-A9OT TCGA-VN-A88L TCGA-VP-A875 TCGA-VP-AA1N TCGA-YL-A8SJ TCGA-YL-A8SL 
       15.65        24.53        75.91        44.88        45.86        32.45 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9L5 TCGA-ZG-A9L9 
       62.79        14.04        24.33         4.27        29.85        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       12.43        22.75        17.98 

$`DEL PEAK  1(1P31.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
       22.06        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 
       13.02        15.98        26.99         9.99        32.02         2.99 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 
       27.16        33.11        19.56        13.32        29.79        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-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        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        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        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1.78        41.62        81.04        67.99        66.67        83.87 
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-G9-6362 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-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        64.18        52.93 
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 
       23.93         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       36.36        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.15         1.78         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        9.53        25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 
       11.57       113.10        56.28        44.68       115.86       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       67.59        49.25        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       69.27        26.43        66.18       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23         5.69        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA 
       30.38        15.58         6.64        58.39         6.71        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9OY 
       38.93        41.19        19.36        12.20         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78        16.31       111.39       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        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 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        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        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       28.77        53.06        46.29       114.38        71.34         8.98 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        60.99        62.37        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        19.17         3.78        16.96        19.04        12.16 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                         0.76                          0.72 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                       115.13                        165.17 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                        29.85                         26.17 
[1] "0.8 - 115.1 (29.9)" "0.7 - 165.2 (26.2)"
[1] "hr=" "1.8"
D29V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  1(1P31.3) MUTATED    13  42   2
  DEL PEAK  1(1P31.3) WILD-TYPE 175 239   8
D29V3, multiclass
    clus
vv   DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  T2                          13                           175
  T3                          42                           239
  T4                           2                             8
[1] 3 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    38  13
  DEL PEAK  1(1P31.3) WILD-TYPE 300  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P31.3) MUTATED     38   13
  DEL PEAK  1(1P31.3) WILD-TYPE  300   62
   clus
vv  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  0                          38                           300
  1                          13                            62
[1] 2 2
[1] FALSE
D29V5, binary
                               cls
clus                              0   1
  DEL PEAK  1(1P31.3) MUTATED     0  57
  DEL PEAK  1(1P31.3) WILD-TYPE  14 411
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P31.3) MUTATED      0   57
  DEL PEAK  1(1P31.3) WILD-TYPE   14  411
                                        clus
vv                                       DEL PEAK  1(1P31.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             57
                                        clus
vv                                       DEL PEAK  1(1P31.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              411
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  1(1P31.3) MUTATED    29  24   1   2
  DEL PEAK  1(1P31.3) WILD-TYPE 281 114   4  13
D29V6, multiclass
    clus
vv   DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  R0                          29                           281
  R1                          24                           114
  R2                           1                             4
  RX                           2                            13
[1] 4 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    55   0
  DEL PEAK  2(1P22.1) WILD-TYPE 418   8
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           55                           426 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            0                             8 
$`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        36.13        25.68        14.14        38.10 
TCGA-EJ-8472 TCGA-FC-7961 TCGA-G9-6332 TCGA-G9-6338 TCGA-G9-6351 TCGA-G9-6369 
       24.85        15.42        87.35        66.67        46.16        39.95 
TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7745 TCGA-HC-8257 TCGA-HC-A6HY 
       65.26        40.08         0.72        23.70        23.87         4.41 
TCGA-J4-A67N TCGA-J9-A8CL TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E6 TCGA-KK-A8I5 
       16.54        13.32        86.40        30.02       113.33       101.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IK 
       32.91        63.48         2.73        82.36        66.18        51.39 
TCGA-M7-A725 TCGA-V1-A8MG TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-VN-A88L TCGA-VP-A875 
       18.84        28.18        22.55        79.73        24.53        75.91 
TCGA-VP-A878 TCGA-VP-AA1N TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XK-AAJT TCGA-YL-A8HM 
       97.41        44.88        37.05        38.04        47.15        48.72 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WL 
       45.86        32.45        62.79         8.98        14.04        24.33 
TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LM TCGA-ZG-A9LZ 
       13.28         4.27        11.67        29.85        12.43        22.75 
TCGA-ZG-A9ND 
       13.48 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5761 
       24.03         1.02        13.02        35.01        31.00         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-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        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-8474 
        3.75        23.05        19.92        77.16        76.41        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       49.81        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-G9-6370 
       45.30        39.39        44.81         3.32        40.18        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        58.45        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        64.18        50.73        52.93 
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        23.93         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        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 
       28.60         1.68         2.37        38.17        44.55         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
       31.69        23.57         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        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 
       24.56        31.43        19.36        22.42        28.27         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        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        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12        13.87         5.85        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       56.28        44.68       115.86        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
      115.13        49.25        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94        67.99        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8II 
       65.82        31.79        67.43        69.27        26.43       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        30.38        15.58         6.64        58.39 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
        6.71        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M 
       49.87         4.70         5.82         8.84        25.51         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      111.39       109.58        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       32.19         3.91        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       41.39        36.95        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        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        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       46.29       114.38        71.34        53.36        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9L2 
       49.91        28.34         3.09        14.53        10.13        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       36.43        22.59        20.28        19.17         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       19.04        12.16        17.98        14.96        11.47         4.34 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         0.72                          0.76 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       113.33                        165.17 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        30.02                         26.17 
[1] "0.7 - 113.3 (30.0)" "0.8 - 165.2 (26.2)"
[1] "hr="     "8.8e+07"
D30V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  2(1P22.1) MUTATED    11  42   2
  DEL PEAK  2(1P22.1) WILD-TYPE 177 239   8
D30V3, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T2                          11                           177
  T3                          42                           239
  T4                           2                             8
[1] 3 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    38  13
  DEL PEAK  2(1P22.1) WILD-TYPE 300  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     38   13
  DEL PEAK  2(1P22.1) WILD-TYPE  300   62
   clus
vv  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  0                          38                           300
  1                          13                            62
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED     0  55
  DEL PEAK  2(1P22.1) WILD-TYPE  14 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      0   55
  DEL PEAK  2(1P22.1) WILD-TYPE   14  413
                                        clus
vv                                       DEL PEAK  2(1P22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             55
                                        clus
vv                                       DEL PEAK  2(1P22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              413
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P22.1) MUTATED    28  19   0   4
  DEL PEAK  2(1P22.1) WILD-TYPE 282 119   5  11
D30V6, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  R0                          28                           282
  R1                          19                           119
  R2                           0                             5
  RX                           4                            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"
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    27   1
  DEL PEAK  3(1Q23.1) WILD-TYPE 446   7
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           28                           453 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                            1                             7 
$`DEL PEAK  3(1Q23.1) MUTATED`
TCGA-2A-AAYF TCGA-EJ-5525 TCGA-EJ-7115 TCGA-EJ-7315 TCGA-EJ-A8FS TCGA-FC-7961 
       31.96        36.66        88.34        33.14         8.75        15.42 
TCGA-HC-7075 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7744 TCGA-HC-7752 TCGA-HC-8257 
       19.76        36.36        14.47         1.68        25.71        23.87 
TCGA-J4-A67M TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A8I9 TCGA-KK-A8IA 
       30.94        19.66        56.28        30.02        32.91        63.48 
TCGA-KK-A8IG TCGA-V1-A8X3 TCGA-VN-A943 TCGA-VP-A87B TCGA-XK-AAJA TCGA-XK-AAJP 
       82.36         6.64        16.31        85.18        30.58        41.39 
TCGA-YL-A8S8 TCGA-YL-A8SH TCGA-ZG-A9L6 TCGA-ZG-A9LM 
       62.14        28.77        22.59        12.43 

$`DEL PEAK  3(1Q23.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       25.35        30.31        20.22        11.51         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-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-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        29.06        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       37.81        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        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-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 
        4.21        10.82         9.27         9.83         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        13.45        22.36        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 
       83.87        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        58.45        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        64.18        50.73        52.93 
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-7078 
       26.01        23.93         6.08        30.94         3.68        65.26 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.93        37.35        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       31.69        23.57         1.48        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.97        17.16        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 
       31.43        19.36        22.42        28.27         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        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 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        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        33.01 
TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       25.32        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68        86.40       115.86        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IB TCGA-KK-A8IC 
      101.79        21.96        65.82        31.79         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       69.27        26.43        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       19.36        12.20        15.65         8.42         5.59         4.27 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        6.15        17.75        49.87         4.70         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
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        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJR 
       31.99        31.96        37.25        40.04        41.49        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        51.45        48.72        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       37.94        36.43        29.85        20.28        19.17         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                         1.68                          0.72 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                        88.34                        165.17 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                         30.3                          26.3 
[1] "1.7 - 88.3 (30.3)"  "0.7 - 165.2 (26.3)"
[1] "hr=" "2.8"
D31V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  3(1Q23.1) MUTATED     8  20   0
  DEL PEAK  3(1Q23.1) WILD-TYPE 180 261  10
D31V3, multiclass
    clus
vv   DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  T2                           8                           180
  T3                          20                           261
  T4                           0                            10
[1] 3 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    22   4
  DEL PEAK  3(1Q23.1) WILD-TYPE 316  71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q23.1) MUTATED     22    4
  DEL PEAK  3(1Q23.1) WILD-TYPE  316   71
   clus
vv  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  0                          22                           316
  1                           4                            71
[1] 2 2
[1] FALSE
D31V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(1Q23.1) MUTATED     0  28
  DEL PEAK  3(1Q23.1) WILD-TYPE  14 440
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q23.1) MUTATED      0   28
  DEL PEAK  3(1Q23.1) WILD-TYPE   14  440
                                        clus
vv                                       DEL PEAK  3(1Q23.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             28
                                        clus
vv                                       DEL PEAK  3(1Q23.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              440
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1Q23.1) MUTATED    18   7   0   2
  DEL PEAK  3(1Q23.1) WILD-TYPE 292 131   5  13
D31V6, multiclass
    clus
vv   DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  R0                          18                           292
  R1                           7                           131
  R2                           0                             5
  RX                           2                            13
[1] 4 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    41   5
  DEL PEAK  4(1Q42.3) WILD-TYPE 432   3
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           46                           435 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                            5                             3 
$`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 
       74.10         6.28        38.10        39.39        58.45        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-J4-AATZ TCGA-J9-A8CL TCGA-KK-A6E5 TCGA-KK-A7AQ 
       43.69        27.39        13.55        13.32        49.25        52.93 
TCGA-KK-A7AV TCGA-KK-A8I5 TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IL 
       27.02       101.79        82.36        66.18       113.98        20.65 
TCGA-M7-A724 TCGA-QU-A6IO TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A9OL TCGA-V1-A9ZR 
       29.23       122.17        28.18        39.29        19.36         5.82 
TCGA-VP-A878 TCGA-WW-A8ZI TCGA-XK-AAJR TCGA-YL-A8SH TCGA-YL-A8SK TCGA-YL-A8SQ 
       97.41        14.76        36.95        28.77        46.29        62.79 
TCGA-YL-A8SR TCGA-ZG-A8QY TCGA-ZG-A9L0 TCGA-ZG-A9L9 
        8.98        13.28        11.67        20.28 

$`DEL PEAK  4(1Q42.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5738 
       25.35        31.96        30.31        20.22        11.51         6.97 
TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
       22.06        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00        23.01         1.02        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-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-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        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        35.18        30.35        27.68        24.39        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-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       77.16        76.41        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        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-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        23.93         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-7211 
       65.26         2.93        36.36        37.35        14.47         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.88         1.15         0.76         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T 
       30.94        16.54        27.58        32.05        29.92         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        14.37        20.28        11.77        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU 
      115.13       113.33        67.07        58.19         6.44        58.36 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       29.56        20.94        67.99        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        51.39        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       13.15        34.85        25.08        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       140.19        86.14        18.12        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       41.23        40.44        16.70        14.73        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       30.38        15.58        22.55         6.64        58.39        79.73 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT 
        6.71        20.91        38.93        41.19        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        4.70         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       75.91       109.58        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        44.88        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        30.58        41.39        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
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        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        53.06        45.86        32.45       114.38        71.34 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
       28.34         3.09        14.53        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       36.43        29.85        22.59        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                         0.72                          0.76 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                       122.17                        165.17 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                        28.36                         26.04 
[1] "0.7 - 122.2 (28.4)" "0.8 - 165.2 (26.0)"
[1] "hr=" "11" 
D32V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  4(1Q42.3) MUTATED    16  28   2
  DEL PEAK  4(1Q42.3) WILD-TYPE 172 253   8
D32V3, multiclass
    clus
vv   DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  T2                          16                           172
  T3                          28                           253
  T4                           2                             8
[1] 3 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    33  11
  DEL PEAK  4(1Q42.3) WILD-TYPE 305  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.3) MUTATED     33   11
  DEL PEAK  4(1Q42.3) WILD-TYPE  305   64
   clus
vv  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  0                          33                           305
  1                          11                            64
[1] 2 2
[1] FALSE
D32V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(1Q42.3) MUTATED     1  45
  DEL PEAK  4(1Q42.3) WILD-TYPE  13 423
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.3) MUTATED      1   45
  DEL PEAK  4(1Q42.3) WILD-TYPE   13  423
                                        clus
vv                                       DEL PEAK  4(1Q42.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             45
                                        clus
vv                                       DEL PEAK  4(1Q42.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              423
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(1Q42.3) MUTATED    20  22   0   2
  DEL PEAK  4(1Q42.3) WILD-TYPE 290 116   5  13
D32V6, multiclass
    clus
vv   DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  R0                          20                           290
  R1                          22                           116
  R2                           0                             5
  RX                           2                            13
[1] 4 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    44   1
  DEL PEAK  5(2P21) WILD-TYPE 429   7
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         45                         436 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                          1                           7 
$`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        36.13 
TCGA-EJ-A46F TCGA-FC-7961 TCGA-G9-7525 TCGA-HC-7213 TCGA-HC-7747 TCGA-HC-7749 
       25.74        15.42        32.68        40.08        24.59         1.97 
TCGA-HC-7819 TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A76W TCGA-J4-A67M TCGA-J9-A8CL 
       17.85        23.87        22.36         7.00        30.94        13.32 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-TP-A8TV 
      113.10        56.28       115.13       113.33        49.94        13.32 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WS TCGA-V1-A9OL TCGA-V1-A9ZR TCGA-VP-A875 
       14.73        53.16        15.58        19.36         5.82        75.91 
TCGA-VP-A87D TCGA-XJ-A83F TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SC 
       60.92        37.05        47.15        71.77        16.83        41.46 
TCGA-YL-A8SJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-ZG-A8QY TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       45.86        62.37        24.33        13.28        11.67        29.85 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       22.75        17.98        13.48 

$`DEL PEAK  5(2P21) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       45.73        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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-5525 
       47.80        52.27        64.50        51.88        68.35        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        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       74.10        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       25.18        21.60        20.58        17.23        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        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        83.87        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        58.45        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        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        28.18        26.01        23.93         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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       37.35        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        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7750 
       23.57         1.48         1.68        23.70        26.04        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       25.71        30.51        30.84        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       22.42        28.27         2.17         2.27        22.55        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-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        33.01        25.32        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       11.77        13.55        27.12        13.87         5.85        10.62 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       11.57        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      165.17        67.59        49.25        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 
       52.93        58.36        27.02        34.65        51.68        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       18.12        11.90        41.23        28.18        40.44        16.70 
TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       39.29        52.08        30.38        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ 
       79.73         6.71        20.91        38.93        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       49.87         4.70         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        53.36        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47        32.19         3.91        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        30.58        41.39        36.95        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       62.14        60.56        56.52        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        53.36        60.99        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       14.53        10.13         4.27        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.16        14.96        11.47         4.34 

  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                       1.02                        0.72 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     115.13                      165.17 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     28.930                      26.545 
[1] "1.0 - 115.1 (28.9)" "0.7 - 165.2 (26.5)"
[1] "hr=" "1.1"
D33V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  5(2P21) MUTATED     7  35   3
  DEL PEAK  5(2P21) WILD-TYPE 181 246   7
D33V3, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  T2                         7                         181
  T3                        35                         246
  T4                         3                           7
[1] 3 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    30  13
  DEL PEAK  5(2P21) WILD-TYPE 308  62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     30   13
  DEL PEAK  5(2P21) WILD-TYPE  308   62
   clus
vv  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  0                        30                         308
  1                        13                          62
[1] 2 2
[1] FALSE
D33V5, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     0  45
  DEL PEAK  5(2P21) WILD-TYPE  14 423
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      0   45
  DEL PEAK  5(2P21) WILD-TYPE   14  423
                                        clus
vv                                       DEL PEAK  5(2P21) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           45
                                        clus
vv                                       DEL PEAK  5(2P21) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            423
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  5(2P21) MUTATED    21  19   1   2
  DEL PEAK  5(2P21) WILD-TYPE 289 119   4  13
D33V6, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  R0                        21                         289
  R1                        19                         119
  R2                         1                           4
  RX                         2                          13
[1] 4 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    88   2
  DEL PEAK  6(2Q22.1) WILD-TYPE 385   6
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           90                           391 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                            2                             6 
$`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 
       74.10        83.57        33.14         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        36.36        40.08         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-HC-A76W TCGA-HI-7171 TCGA-J4-A83J TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP 
        7.00        43.69        22.88        13.32        40.67        12.69 
TCGA-KC-A7F3 TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 
       21.86        86.40        30.02       115.13        49.25        58.19 
TCGA-KK-A7AQ TCGA-KK-A7B0 TCGA-KK-A7B3 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IG 
       52.93        32.84        29.56        63.48        26.43        82.36 
TCGA-KK-A8IK TCGA-M7-A724 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8MM TCGA-V1-A8WS 
       51.39        29.23        41.00        13.32        39.29        15.58 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9Z9 
       79.73         6.71        19.36        12.20         8.42        17.75 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-AA1N 
       25.78       111.39        75.91        97.41        85.18        44.88 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XK-AAJP TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HM 
        3.91        38.04        41.39        47.15        25.48        48.72 
TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A9WI TCGA-YL-A9WK 
       71.77        45.86        32.45       114.38        53.36        62.37 
TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
       28.34        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       29.85        19.17        12.43        22.75        17.98        13.48 

$`DEL PEAK  6(2Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-2A-AAYF 
       20.42        43.79        32.71        22.06        25.35        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       30.31        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 
       44.02        12.00         1.02        23.01         1.02        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-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-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-7125 
       60.23        41.85        47.87        29.06        88.34        93.70 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       36.13        37.81        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 
       30.35        27.68        24.39        23.90        25.87        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-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB 
        8.75         4.54         4.31         4.77        28.41        22.36 
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        83.87        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-G9-6370 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        58.45 
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        64.18        52.93 
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        23.93 
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        65.26         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       37.35        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         2.10        31.69        23.57         1.48 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        26.04        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       28.27         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL 
        1.58        15.88        22.36         0.76         1.78         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         3.48         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       25.28        27.91        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
        5.85        10.62        15.22        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
      113.10        56.28        44.68       115.86        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
       67.59       113.33        67.07         6.44        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B4 
       34.65        51.68        49.94        34.95        36.13        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
        2.73        67.43        69.27        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       34.85        25.08        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        86.14        18.12        11.90        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       40.44        16.70        14.73        53.16        52.08        30.38 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       22.55         6.64        58.39        20.91        38.93        41.19 
TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       15.65         5.59         4.27         6.15        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A879 
       15.81        41.42        44.91        16.31       109.58        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        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI 
       14.76        45.47        32.19        37.05        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-YJ-A8SW 
       41.49        30.58        36.95        51.81        32.19         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       52.96        49.02        51.45        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        53.06        46.29 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WL 
       71.34        62.79         8.98        14.04        60.99        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       49.91         3.09        37.94        36.43        22.59        20.28 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        16.96        19.04        12.16        14.96        11.47 
TCGA-ZG-A9NI 
        4.34 

  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                         0.72                          0.76 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                       115.13                        165.17 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                        29.08                         26.01 
[1] "0.7 - 115.1 (29.1)" "0.8 - 165.2 (26.0)"
[1] "hr=" "1.2"
D34V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  6(2Q22.1) MUTATED    28  59   3
  DEL PEAK  6(2Q22.1) WILD-TYPE 160 222   7
D34V3, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  T2                          28                           160
  T3                          59                           222
  T4                           3                             7
[1] 3 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    66  15
  DEL PEAK  6(2Q22.1) WILD-TYPE 272  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     66   15
  DEL PEAK  6(2Q22.1) WILD-TYPE  272   60
   clus
vv  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  0                          66                           272
  1                          15                            60
[1] 2 2
[1] FALSE
D34V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED     1  89
  DEL PEAK  6(2Q22.1) WILD-TYPE  13 379
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED      1   89
  DEL PEAK  6(2Q22.1) WILD-TYPE   13  379
                                        clus
vv                                       DEL PEAK  6(2Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             89
                                        clus
vv                                       DEL PEAK  6(2Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              379
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q22.1) MUTATED    50  31   1   4
  DEL PEAK  6(2Q22.1) WILD-TYPE 260 107   4  11
D34V6, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  R0                          50                           260
  R1                          31                           107
  R2                           1                             4
  RX                           4                            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"
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    81   2
  DEL PEAK  7(2Q22.3) WILD-TYPE 392   6
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           83                           398 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                            2                             6 
$`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        74.10        36.13         6.28        25.68        18.15 
TCGA-EJ-8470 TCGA-EJ-A65M TCGA-EJ-A8FN TCGA-G9-6333 TCGA-G9-6496 TCGA-G9-6499 
       38.10         7.56        10.82        81.04        56.75        50.73 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7744 
       65.26        36.36        28.54        40.08         2.37         1.68 
TCGA-HC-7749 TCGA-HC-8257 TCGA-HC-8261 TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AP 
        1.97        23.87        17.95         1.15         2.01         2.33 
TCGA-HC-A76W TCGA-HI-7171 TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KK-A6E0 TCGA-KK-A6E4 
        7.00        43.69        13.32        12.69        30.02       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7B3 TCGA-KK-A8IA TCGA-KK-A8IG 
       49.25        58.19        52.93        29.56        63.48        82.36 
TCGA-KK-A8IH TCGA-KK-A8IK TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8MM TCGA-V1-A8WN 
       66.18        51.39        41.00        13.32        39.29        30.38 
TCGA-V1-A8WS TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9Z9 TCGA-VN-A943 
       15.58        38.93        12.20         8.42        17.75        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-XA-A8JR TCGA-XJ-A83G 
      111.39        75.91        97.41        85.18         3.91        38.04 
TCGA-XK-AAIV TCGA-XK-AAJP TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HM TCGA-YL-A8HO 
       37.25        41.39        47.15        25.48        48.72        71.77 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WY 
       45.86        32.45       114.38         8.98        62.37        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB 
       14.53        10.13         4.27        11.67        29.85        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       12.43        12.16        22.75        17.98        13.48 

$`DEL PEAK  7(2Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03        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-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-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       38.53        60.23        46.55        47.80        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-7125 TCGA-EJ-7218 
       41.85        47.87        29.06        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68        24.39        23.90        38.37        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-8472 TCGA-EJ-8474 
       23.05        19.92        77.16        76.41        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        6.48        15.65         4.21         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        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-G9-6498 TCGA-G9-7509 
       58.45        25.15        27.29        58.22        64.18        52.93 
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        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.93        37.35        14.47         0.79        28.60         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 
        1.48        23.70        24.59        26.04        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 
       22.42        28.27         2.17         2.27        22.55        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL 
        1.58        15.88        22.36         0.76         1.78         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         3.48         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL 
       13.87         5.85        10.62        15.22        40.67        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 
       86.40       115.86        54.54       165.17        67.59       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       67.07         6.44        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B4 TCGA-KK-A8I4 
       49.94        32.84        34.95        36.13        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB 
      101.79        21.96        65.82        31.79        32.91         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL 
       67.43        69.27        26.43       113.98        51.25        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        86.14        18.12        11.90        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WV 
       40.44        16.70        14.73        53.16        52.08        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OH 
        6.64        58.39        79.73         6.71        20.91        41.19 
TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZG 
       19.36        15.65         5.59         4.27         6.15        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A876 
       15.52        15.81        41.42        44.91        25.78       109.58 
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        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83F 
       42.94        44.88        14.76        45.47        32.19        37.05 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       40.04        41.49        30.58        36.95        51.81        32.19 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 
        4.87        52.96        49.02        51.45        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       46.29        71.34        62.79        14.04        53.36        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       24.33        49.91         3.09        13.28        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9MC 
       22.59        20.28         3.78        16.96        19.04        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       11.47         4.34 

  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                         1.02                          0.72 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                       115.13                        165.17 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                       29.560                        26.025 
[1] "1.0 - 115.1 (29.6)" "0.7 - 165.2 (26.0)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  7(2Q22.3) MUTATED    30  50   3
  DEL PEAK  7(2Q22.3) WILD-TYPE 158 231   7
D35V3, multiclass
    clus
vv   DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  T2                          30                           158
  T3                          50                           231
  T4                           3                             7
[1] 3 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    58  15
  DEL PEAK  7(2Q22.3) WILD-TYPE 280  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.3) MUTATED     58   15
  DEL PEAK  7(2Q22.3) WILD-TYPE  280   60
   clus
vv  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  0                          58                           280
  1                          15                            60
[1] 2 2
[1] FALSE
D35V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.3) MUTATED     1  82
  DEL PEAK  7(2Q22.3) WILD-TYPE  13 386
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.3) MUTATED      1   82
  DEL PEAK  7(2Q22.3) WILD-TYPE   13  386
                                        clus
vv                                       DEL PEAK  7(2Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             82
                                        clus
vv                                       DEL PEAK  7(2Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              386
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(2Q22.3) MUTATED    48  28   1   3
  DEL PEAK  7(2Q22.3) WILD-TYPE 262 110   4  12
D35V6, multiclass
    clus
vv   DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  R0                          48                           262
  R1                          28                           110
  R2                           1                             4
  RX                           3                            12
[1] 4 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    75   1
  DEL PEAK  8(3P13) WILD-TYPE 398   7
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         76                         405 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                          1                           7 
$`DEL PEAK  8(3P13) MUTATED`
TCGA-2A-A8VV TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5746 
       22.06        20.22         6.97        22.06        12.99        24.03 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5764 TCGA-EJ-5497 TCGA-EJ-5501 TCGA-EJ-5505 
       31.00         1.02         1.02        13.32        44.88        30.31 
TCGA-EJ-5510 TCGA-EJ-5517 TCGA-EJ-5542 TCGA-EJ-7327 TCGA-EJ-7788 TCGA-EJ-7797 
       36.69        47.80        29.06        30.35        14.14        19.92 
TCGA-EJ-8469 TCGA-EJ-A65D TCGA-G9-6332 TCGA-G9-6354 TCGA-G9-6362 TCGA-G9-6363 
       76.41        12.92        87.35        49.35        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6384 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-A6BY TCGA-HC-7747 
       39.39        25.15        28.18        23.93         3.68        24.59 
TCGA-HC-7749 TCGA-HC-8213 TCGA-HC-8259 TCGA-HC-A6AL TCGA-HC-A6HY TCGA-HC-A76W 
        1.97        19.36         2.27         2.20         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83M 
        4.93        25.48        18.84        27.39        16.83        14.37 
TCGA-J4-AATZ TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E6 TCGA-KK-A7AZ 
       13.55        44.68        54.54       165.17       113.33        49.94 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A8II TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 
       34.95        29.56       113.98        47.28        21.14        18.84 
TCGA-QU-A6IM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A9O7 TCGA-V1-A9OA 
       41.00        53.16        30.38        15.58        79.73        20.91 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 
       24.53         6.21        44.91        16.31        75.91       109.58 
TCGA-VP-A87K TCGA-XK-AAK1 TCGA-YL-A8HK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ 
       42.94        32.19        49.02        32.45        71.34        62.79 
TCGA-YL-A9WL TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       24.33        12.43        22.75        11.47 

$`DEL PEAK  8(3P13) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5743 
       31.96        30.31        11.51         2.99         1.02        13.97 
TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 
        1.97         1.02        13.02        35.01         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00        23.01         1.02        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-5498 TCGA-EJ-5499 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 
       29.79        46.52        26.30        45.73        28.93        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       23.90        38.93        48.13        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        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        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
        3.75        23.05        77.16        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        23.34        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        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-G9-6365 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-G9-6385 TCGA-G9-6494 
       26.66        31.50        37.97        58.45        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        32.68        26.01         6.08        30.94 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        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        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 
        1.48         1.68        23.70        26.04        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        31.43        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       28.27        23.87         2.17        22.55        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-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         9.53        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       27.58        32.05        29.92         6.02        25.28        27.91 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        20.28        11.77 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12        13.87         5.85        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E3 
      113.10        56.28        86.40       115.86        30.02        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
      115.13        49.25        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B2 
       58.36        27.02        34.65        51.68        32.84        36.13 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       82.36        66.18        51.25        51.39        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC 
       12.62        13.15        34.85        25.08        29.23         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        3.19       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 
       39.29        52.08        22.55         6.64        58.39         6.71 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        41.19        19.36        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        5.82         8.84        25.51        15.52        15.81        41.42 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       25.78       111.39        97.41        23.93        85.18        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        53.36        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM 
       51.81        25.48         4.87        52.96        51.45        48.72 
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        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO 
       45.14        28.77        53.06        45.86        46.29       114.38 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX 
        8.98        14.04        53.36        60.99        62.37        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 
       19.17         3.78        16.96        19.04        12.16        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                       1.02                        0.72 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                     165.17                      140.19 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                     25.315                      26.990 
[1] "1.0 - 165.2 (25.3)" "0.7 - 140.2 (27.0)"
[1] "hr=" "1.6"
D36V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  8(3P13) MUTATED    29  47   1
  DEL PEAK  8(3P13) WILD-TYPE 159 234   9
D36V3, multiclass
    clus
vv   DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  T2                        29                         159
  T3                        47                         234
  T4                         1                           9
[1] 3 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    58   9
  DEL PEAK  8(3P13) WILD-TYPE 280  66
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3P13) MUTATED     58    9
  DEL PEAK  8(3P13) WILD-TYPE  280   66
   clus
vv  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  0                        58                         280
  1                         9                          66
[1] 2 2
[1] FALSE
D36V5, binary
                             cls
clus                            0   1
  DEL PEAK  8(3P13) MUTATED     4  73
  DEL PEAK  8(3P13) WILD-TYPE  10 395
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3P13) MUTATED      4   73
  DEL PEAK  8(3P13) WILD-TYPE   10  395
                                        clus
vv                                       DEL PEAK  8(3P13) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           73
                                        clus
vv                                       DEL PEAK  8(3P13) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            395
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  8(3P13) MUTATED    54  18   0   4
  DEL PEAK  8(3P13) WILD-TYPE 256 120   5  11
D36V6, multiclass
    clus
vv   DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  R0                        54                         256
  R1                        18                         120
  R2                         0                           5
  RX                         4                          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"
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    32   0
  DEL PEAK  9(3Q29) WILD-TYPE 441   8
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         32                         449 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                          0                           8 
$`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        21.96 
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        31.43        23.87        12.30        44.68       113.33 
TCGA-KK-A7AQ TCGA-V1-A9OH TCGA-V1-A9OY TCGA-V1-A9ZR TCGA-VN-A88R TCGA-VP-A876 
       52.93        41.19         5.59         5.82        25.78       109.58 
TCGA-YL-A8HK TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-ZG-A8QZ TCGA-ZG-A9L2 
       49.02        46.29        32.45        62.79        10.13        37.94 
TCGA-ZG-A9L5 TCGA-ZG-A9LB 
       29.85        19.17 

$`DEL PEAK  9(3Q29) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       43.79        32.71        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         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-5767 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06         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-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       19.56        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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        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-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
       23.80        21.96        23.34        12.92        13.71        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        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-G9-6362 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 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.34 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        23.93         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 
       65.26         2.93        36.36        37.35        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        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       25.71        30.51        30.84        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       28.27         2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       20.28        11.77        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       19.66         8.88        11.57       113.10        56.28        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
       49.25        67.07        58.19         6.44        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       19.36        12.20        15.65         8.42         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       17.75        49.87         4.70         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 
        6.21        15.52        15.81        41.42        44.91        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      111.39        75.91        97.41        23.93        85.18        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        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        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 
       56.52        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34         8.98        14.04        53.36        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       13.28         4.27        11.67        36.43        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                       5.59                        0.72 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                     113.33                      165.17 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                      28.62                       26.43 
[1] "5.6 - 113.3 (28.6)" "0.7 - 165.2 (26.4)"
[1] "hr="     "2.7e+07"
D37V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  9(3Q29) MUTATED    11  19   2
  DEL PEAK  9(3Q29) WILD-TYPE 177 262   8
D37V3, multiclass
    clus
vv   DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  T2                        11                         177
  T3                        19                         262
  T4                         2                           8
[1] 3 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    23   8
  DEL PEAK  9(3Q29) WILD-TYPE 315  67
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(3Q29) MUTATED     23    8
  DEL PEAK  9(3Q29) WILD-TYPE  315   67
   clus
vv  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  0                        23                         315
  1                         8                          67
[1] 2 2
[1] FALSE
D37V5, binary
                             cls
clus                            0   1
  DEL PEAK  9(3Q29) MUTATED     2  30
  DEL PEAK  9(3Q29) WILD-TYPE  12 438
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(3Q29) MUTATED      2   30
  DEL PEAK  9(3Q29) WILD-TYPE   12  438
                                        clus
vv                                       DEL PEAK  9(3Q29) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           30
                                        clus
vv                                       DEL PEAK  9(3Q29) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            438
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  9(3Q29) MUTATED    16  12   1   1
  DEL PEAK  9(3Q29) WILD-TYPE 294 126   4  14
D37V6, multiclass
    clus
vv   DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  R0                        16                         294
  R1                        12                         126
  R2                         1                           4
  RX                         1                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    49   0
  DEL PEAK 10(4Q28.2) WILD-TYPE 424   8
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           49                           432 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                            0                             8 
$`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        74.10 
TCGA-EJ-7312 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7789 TCGA-EJ-A65B 
       36.13         6.28        24.39        38.37        18.15        23.34 
TCGA-FC-7961 TCGA-G9-6361 TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-7738 TCGA-HC-A48F 
       15.42        46.52        50.73        36.36        31.69        22.36 
TCGA-HC-A6AO TCGA-J9-A52B TCGA-J9-A8CP TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E8 
       17.42        13.87        12.69        86.40        30.02        58.19 
TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IK TCGA-M7-A721 TCGA-M7-A722 TCGA-V1-A8MG 
       32.91         2.73        51.39        13.15        34.85        28.18 
TCGA-V1-A9O5 TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-VN-A88P TCGA-VP-A87K TCGA-VP-AA1N 
       58.39         4.27        17.75        41.42        42.94        44.88 
TCGA-XJ-A83G TCGA-XK-AAIR TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8SL 
       38.04        31.96        30.58        47.15        48.72        32.45 
TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       14.04        24.33        20.28        12.43        22.75        17.98 
TCGA-ZG-A9N3 
       11.47 

$`DEL PEAK 10(4Q28.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        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-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
       15.06        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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        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-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        88.34 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 
       27.09        35.18        30.35        27.68        23.90        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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       21.96        23.80        21.96        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45        22.36        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        83.87 
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-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       49.35        47.15        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        58.45        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        64.18        52.93        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        23.93         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        65.26         2.93        37.35 
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        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 
        2.37        38.17        44.55         0.72         2.10        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        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-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       27.12         5.85        10.62        13.32        15.22        40.67 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        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       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       65.82        31.79        63.48        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36        66.18       113.98        51.25        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        5.19        21.14        12.62        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK 
       18.12        11.90        13.32        41.23        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
       22.55         6.64        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
        6.15        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R 
       24.53         6.21        15.52        15.81        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H 
       14.76        45.47        32.19         3.91        37.05        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.49        41.39        36.95        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
        4.87        52.96        49.02        51.45        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        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        45.86        46.29       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        53.36        60.99        62.37        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       37.94        36.43        29.85        22.59        19.17         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        19.04        12.16        14.96        13.48         4.34 

  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                         2.73                          0.72 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                        86.40                        165.17 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                        31.69                         25.94 
[1] "2.7 - 86.4 (31.7)"  "0.7 - 165.2 (25.9)"
[1] "hr="     "7.9e+07"
D38V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 10(4Q28.2) MUTATED    15  31   3
  DEL PEAK 10(4Q28.2) WILD-TYPE 173 250   7
D38V3, multiclass
    clus
vv   DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  T2                          15                           173
  T3                          31                           250
  T4                           3                             7
[1] 3 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    34  10
  DEL PEAK 10(4Q28.2) WILD-TYPE 304  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q28.2) MUTATED     34   10
  DEL PEAK 10(4Q28.2) WILD-TYPE  304   65
   clus
vv  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  0                          34                           304
  1                          10                            65
[1] 2 2
[1] FALSE
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q28.2) MUTATED     2  47
  DEL PEAK 10(4Q28.2) WILD-TYPE  12 421
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q28.2) MUTATED      2   47
  DEL PEAK 10(4Q28.2) WILD-TYPE   12  421
                                        clus
vv                                       DEL PEAK 10(4Q28.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             47
                                        clus
vv                                       DEL PEAK 10(4Q28.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              421
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q28.2) MUTATED    27  18   0   2
  DEL PEAK 10(4Q28.2) WILD-TYPE 283 120   5  13
D38V6, multiclass
    clus
vv   DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  R0                          27                           283
  R1                          18                           120
  R2                           0                             5
  RX                           2                            13
[1] 4 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    93   2
  DEL PEAK 11(5Q11.2) WILD-TYPE 380   6
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           95                           386 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                            2                             6 
$`DEL PEAK 11(5Q11.2) MUTATED`
TCGA-2A-A8VT TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5765 
       32.71        20.22        11.51        35.01         0.92        23.01 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5792 TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5509 
        1.02        24.03         2.99        44.88        23.90        48.13 
TCGA-EJ-5519 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7115 TCGA-EJ-7312 TCGA-EJ-7325 
       64.50        36.66        38.76        88.34        36.13        35.18 
TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A65M TCGA-FC-A4JI 
       18.15        77.16        24.85        25.18         7.56        13.45 
TCGA-G9-6338 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-H9-7775 TCGA-HC-7078 
       66.67        50.73        38.96        30.97         6.08        65.26 
TCGA-HC-7821 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A8D1 TCGA-HI-7168 
       31.43         1.58         1.15        22.36        18.84        78.61 
TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A7FA TCGA-KK-A59X 
       22.88        13.87        13.32        15.22        19.66        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A7AQ TCGA-KK-A7AU 
       44.68        86.40        30.02        54.54        52.93        58.36 
TCGA-KK-A7B0 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IA 
       32.84        20.94       101.79        65.82        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-QU-A6IN 
        2.73        26.43        66.18       113.98        51.39       140.19 
TCGA-TP-A8TV TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OT TCGA-V1-A9ZI 
       13.32        22.55        58.39        20.91        15.65         4.70 
TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A87D 
        5.82        25.51        25.78       111.39        97.41        60.92 
TCGA-VP-A87H TCGA-VP-AA1N TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YL-A8HM 
       21.80        44.88        41.49        41.39        47.15        48.72 
TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WL 
       62.14        16.83        28.77       114.38         8.98        24.33 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       11.67        37.94        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        22.75        14.96        11.47        13.48 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       31.96        30.31         2.99         6.97        22.06         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-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       31.00         1.02         2.04        44.02        12.00         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06         2.04        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-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       13.32        29.79        46.52        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       30.31        27.19        38.93        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 
       36.23        60.23        46.55        47.80        52.27        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       68.35        43.07        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       29.06        74.10        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        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-8469 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       19.92        76.41        38.10        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        18.41        21.90        14.83        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        15.42        22.36        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        83.87 
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        58.45        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        64.18        52.93        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        32.68        26.01        23.93        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        36.36        37.35        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        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       17.95        22.32        15.88         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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       27.12         5.85        10.62        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 
        8.88        11.57       113.10       115.86       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        34.65        51.68        49.94        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8ID 
       29.56        67.99        21.96        31.79        67.43        69.27 
TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       82.36        51.25        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19        41.00       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       11.90        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        15.58         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       79.73         6.71        38.93        41.19        19.36        12.20 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87B 
       44.91        16.31        75.91       109.58        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       55.56        66.97        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       30.58        36.95        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SB 
       52.96        49.02        51.45        71.77        60.56        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        53.06        45.86        46.29        32.45 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79        14.04        53.36        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         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY 
        4.27        36.43        22.59         3.78        16.96        12.16 
TCGA-ZG-A9M4 TCGA-ZG-A9NI 
       17.98         4.34 

  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                         0.92                          0.72 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                       140.19                        165.17 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                        28.77                         26.48 
[1] "0.9 - 140.2 (28.8)" "0.7 - 165.2 (26.5)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 11(5Q11.2) MUTATED    16  75   5
  DEL PEAK 11(5Q11.2) WILD-TYPE 172 206   5
D39V3, multiclass
    clus
vv   DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  T2                          16                           172
  T3                          75                           206
  T4                           5                             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"
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q11.2) MUTATED    61  29
  DEL PEAK 11(5Q11.2) WILD-TYPE 277  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q11.2) MUTATED     61   29
  DEL PEAK 11(5Q11.2) WILD-TYPE  277   46
   clus
vv  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  0                          61                           277
  1                          29                            46
[1] 2 2
[1] FALSE
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q11.2) MUTATED     2  94
  DEL PEAK 11(5Q11.2) WILD-TYPE  12 374
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q11.2) MUTATED      2   94
  DEL PEAK 11(5Q11.2) WILD-TYPE   12  374
                                        clus
vv                                       DEL PEAK 11(5Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             94
                                        clus
vv                                       DEL PEAK 11(5Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              374
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(5Q11.2) MUTATED    50  38   1   4
  DEL PEAK 11(5Q11.2) WILD-TYPE 260 100   4  11
D39V6, multiclass
    clus
vv   DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  R0                          50                           260
  R1                          38                           100
  R2                           1                             4
  RX                           4                            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"
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    94   2
  DEL PEAK 12(5Q13.2) WILD-TYPE 379   6
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           96                           385 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                            2                             6 
$`DEL PEAK 12(5Q13.2) MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5766 
       32.71        11.51        35.01         0.92        23.01         1.02 
TCGA-CH-5768 TCGA-CH-5792 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5509 
       24.03         2.99        46.52        44.88        23.90        48.13 
TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-7115 TCGA-EJ-7312 
       46.55        64.50        43.07        38.76        88.34        36.13 
TCGA-EJ-7325 TCGA-EJ-7789 TCGA-EJ-8472 TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI 
       35.18        18.15        24.85         7.56        15.42        13.45 
TCGA-G9-6338 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-7211 TCGA-HC-8216 
       66.67        50.73        38.96        30.97         0.79        22.42 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HI-7168 TCGA-J4-A83J TCGA-J9-A52B 
        1.15        22.36         2.01        78.61        22.88        13.87 
TCGA-J9-A8CL TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 
       13.32         8.65        19.66        56.28        86.40        30.02 
TCGA-KK-A6E1 TCGA-KK-A7AQ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B4 TCGA-KK-A8I5 
       54.54        52.93        32.84        34.95        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF 
       21.96        65.82        32.91        63.48         2.73        26.43 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MU 
       66.18       113.98        51.39        13.32        28.18        53.16 
TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9ZI 
       22.55        58.39        20.91        15.65         8.42         4.70 
TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A87D 
        5.82        25.51        15.52        25.78       111.39        60.92 
TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XK-AAJP TCGA-XK-AAJT 
       21.80        44.88        45.47        38.04        41.39        47.15 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SO 
       48.72        62.14        16.83        28.77        45.86       114.38 
TCGA-YL-A8SR TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L5 
        8.98        24.33        28.34        10.13        11.67        29.85 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       20.28        19.17        12.43        19.04        11.47        13.48 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 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-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-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       19.56        13.32        29.79        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       30.31        27.19        38.93        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 
       36.23        60.23        47.80        52.27        51.88        68.35 
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-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       74.10        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        30.35        27.68         6.28        24.39 
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 
       77.16        76.41        38.10        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.31         4.77        28.41        22.36        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        83.87 
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        58.45        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        64.18        52.93        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        23.93         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        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       31.43        19.36        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV 
       22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.52        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM 
       11.77        13.55        27.12         5.85        10.62        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y 
       43.66        21.86         8.88        11.57       113.10        44.68 
TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
      115.86       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07        58.19         6.44        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I8 
       51.68        49.94        36.13        29.56        67.99        31.79 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       67.43        69.27        82.36        51.25        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MJ 
      122.17        86.14        18.12        11.90        41.23        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       16.70        14.73        39.29        52.08        30.38        15.58 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
        6.64        79.73         6.71        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       12.20         5.59         4.27         6.15        17.75        49.87 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
        8.84        24.53         6.21        15.81        41.42        44.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       16.31        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS 
       55.56        66.97        53.36        42.94        14.76        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
        3.91        37.05        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       31.99        31.96        37.25        40.04        41.49        30.58 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       36.95        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC 
       49.02        51.45        71.77        60.56        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.14        53.06        46.29        32.45        71.34        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A8QW 
       14.04        53.36        60.99        62.37        49.91         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       14.53        13.28         4.27        37.94        36.43        22.59 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        12.16        22.75        17.98        14.96 
TCGA-ZG-A9NI 
        4.34 

  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                         0.79                          0.72 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                       114.38                        165.17 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                       27.305                        26.660 
[1] "0.8 - 114.4 (27.3)" "0.7 - 165.2 (26.7)"
[1] "hr=" "1.4"
D40V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 12(5Q13.2) MUTATED    15  76   5
  DEL PEAK 12(5Q13.2) WILD-TYPE 173 205   5
D40V3, multiclass
    clus
vv   DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  T2                          15                           173
  T3                          76                           205
  T4                           5                             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"
D40V4, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q13.2) MUTATED    66  25
  DEL PEAK 12(5Q13.2) WILD-TYPE 272  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q13.2) MUTATED     66   25
  DEL PEAK 12(5Q13.2) WILD-TYPE  272   50
   clus
vv  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  0                          66                           272
  1                          25                            50
[1] 2 2
[1] FALSE
D40V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q13.2) MUTATED     2  94
  DEL PEAK 12(5Q13.2) WILD-TYPE  12 374
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q13.2) MUTATED      2   94
  DEL PEAK 12(5Q13.2) WILD-TYPE   12  374
                                        clus
vv                                       DEL PEAK 12(5Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             94
                                        clus
vv                                       DEL PEAK 12(5Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              374
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q13.2) MUTATED    54  34   1   4
  DEL PEAK 12(5Q13.2) WILD-TYPE 256 104   4  11
D40V6, multiclass
    clus
vv   DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  R0                          54                           256
  R1                          34                           104
  R2                           1                             4
  RX                           4                            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"
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   103   2
  DEL PEAK 13(5Q21.1) WILD-TYPE 370   6
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                          105                           376 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                            2                             6 
$`DEL PEAK 13(5Q21.1) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VX TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5751 TCGA-CH-5761 
       32.71        33.96        11.51         2.99        35.01         0.92 
TCGA-CH-5766 TCGA-CH-5788 TCGA-CH-5792 TCGA-EJ-5501 TCGA-EJ-5504 TCGA-EJ-5505 
        1.02        26.99         2.99        44.88        28.93        30.31 
TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5521 TCGA-EJ-5531 TCGA-EJ-7123 TCGA-EJ-7312 
       23.90        48.13        51.88        41.85        74.10        36.13 
TCGA-EJ-7315 TCGA-EJ-7325 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 
       33.14        35.18         6.28        24.39        38.37        25.68 
TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A65E TCGA-EJ-A65M 
       18.15        77.16        38.10        24.85        13.71         7.56 
TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6369 TCGA-G9-6496 
        8.75        15.42        13.45        66.67        39.95        56.75 
TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-8216 TCGA-HC-8261 TCGA-HC-8266 TCGA-HC-A48F 
       50.73        36.36        22.42        17.95         1.15        22.36 
TCGA-HC-A6AP TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A8CP TCGA-KC-A7FA TCGA-KK-A59X 
        2.33        78.61        13.87        12.69        19.66        56.28 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A7AQ TCGA-KK-A7B0 TCGA-KK-A7B4 
       86.40        30.02        54.54        52.93        32.84        20.94 
TCGA-KK-A8I6 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG 
       21.96        32.91        63.48         2.73        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-M7-A721 TCGA-QU-A6IM TCGA-QU-A6IN 
       66.18       113.98        51.39        13.15        41.00       140.19 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A9OX 
       11.90        13.32        28.18        39.29        22.55         8.42 
TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 TCGA-VP-A87B 
        4.27         4.70        25.78        16.31        97.41        85.18 
TCGA-VP-AA1N TCGA-XJ-A83G TCGA-XK-AAIR TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       44.88        38.04        31.96        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HM TCGA-YL-A8SA 
       36.95        47.15        32.19        25.48        48.72        16.83 
TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WL TCGA-ZG-A8QX 
       28.77       114.38         8.98        53.36        24.33        14.53 
TCGA-ZG-A8QY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       13.28        11.67        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LU TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        11.47        13.48 

$`DEL PEAK 13(5Q21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       20.42        43.79        22.06         3.68        25.35        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       30.31        20.22         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       13.97         1.97        24.03         1.02        13.02        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-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        15.98         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-5502 TCGA-EJ-5503 TCGA-EJ-5506 
       13.32        29.79        46.52        26.30        45.73        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-5519 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        52.27        64.50        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-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 
       88.34        93.70        83.57        37.81        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 
       27.09        30.35        27.68        23.90        25.87        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-8469 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       19.92        76.41        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.27         9.83         4.54         4.31         4.77        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6370 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        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       25.15        27.29        58.22        64.18        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.93        37.35        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 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
       30.84        17.85        24.56        31.43        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 
       23.87         2.17         2.27        22.55        22.32         1.58 
TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.88         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
       17.42         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        4.93         9.53        25.48        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL 
        5.85        10.62        13.32        15.22        40.67        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 
        8.88        11.57       113.10        44.68       115.86       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
        6.44        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 
       34.95        36.13        29.56        67.99       101.79        65.82 
TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       31.79        67.43        69.27        51.25        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        5.19        21.14        12.62        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         5.69         3.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       41.23        40.44        16.70        14.73        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       30.38        15.58         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I 
        5.59         6.15        17.75        49.87         5.82         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C 
       44.91       111.39        75.91       109.58        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        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47        32.19         3.91        37.05        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJU 
        9.04         2.99        31.99        37.25        40.04        51.81 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
        4.87        52.96        49.02        51.45        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ 
       60.56        56.52        41.46        45.14        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WJ 
       46.29        32.45        71.34        62.79        14.04        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       62.37        49.91        28.34         3.09        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY 
       37.94        36.43        12.43         3.78        16.96        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9NI 
       22.75        17.98        14.96         4.34 

  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                         0.92                          0.72 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                       140.19                        165.17 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                       28.770                        26.025 
[1] "0.9 - 140.2 (28.8)" "0.7 - 165.2 (26.0)"
[1] "hr=" "1"  
D41V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 13(5Q21.1) MUTATED    30  72   3
  DEL PEAK 13(5Q21.1) WILD-TYPE 158 209   7
D41V3, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  T2                          30                           158
  T3                          72                           209
  T4                           3                             7
[1] 3 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    79  19
  DEL PEAK 13(5Q21.1) WILD-TYPE 259  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED     79   19
  DEL PEAK 13(5Q21.1) WILD-TYPE  259   56
   clus
vv  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  0                          79                           259
  1                          19                            56
[1] 2 2
[1] FALSE
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED     2 103
  DEL PEAK 13(5Q21.1) WILD-TYPE  12 365
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED      2  103
  DEL PEAK 13(5Q21.1) WILD-TYPE   12  365
                                        clus
vv                                       DEL PEAK 13(5Q21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            103
                                        clus
vv                                       DEL PEAK 13(5Q21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              365
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.1) MUTATED    68  28   0   5
  DEL PEAK 13(5Q21.1) WILD-TYPE 242 110   5  10
D41V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  R0                          68                           242
  R1                          28                           110
  R2                           0                             5
  RX                           5                            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"
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    40   1
  DEL PEAK 14(6P25.1) WILD-TYPE 433   7
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           41                           440 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                            1                             7 
$`DEL PEAK 14(6P25.1) MUTATED`
TCGA-2A-A8VT TCGA-CH-5740 TCGA-CH-5754 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5504 
       32.71         1.02         2.04        29.79        46.52        28.93 
TCGA-EJ-5507 TCGA-EJ-5524 TCGA-EJ-7123 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7786 
       23.90        43.07        74.10        38.37        25.68        14.53 
TCGA-FC-7708 TCGA-HC-7213 TCGA-HC-7821 TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A632 
       28.41        40.08        31.43        23.87        22.36         2.01 
TCGA-J9-A52B TCGA-J9-A8CL TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A8IC TCGA-KK-A8II 
       13.87        13.32         8.65        19.66        67.43       113.98 
TCGA-KK-A8IM TCGA-V1-A9OA TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VP-A87C 
       47.28        20.91         4.27         4.70         5.82        55.56 
TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WH 
       44.88        71.77        45.14        32.45        62.79        14.04 
TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LM 
       24.33         3.09        29.85        20.28        12.43 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
       22.06        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         1.02         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        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-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       13.32        44.88        26.30        45.73        30.31        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-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
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-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        29.06        88.34        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        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-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        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        83.87 
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        58.45        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        64.18        50.73        52.93        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 
       23.93         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        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        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.88         1.15         0.76         1.78         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        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        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.88        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN 
       13.55        27.12         5.85        10.62        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       21.86         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ 
        2.73        69.27        26.43        82.36        66.18        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       51.39        20.65         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
       41.00       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       13.32        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        58.39        79.73         6.71        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 
       19.36        12.20        15.65         8.42         5.59         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       17.75        49.87         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       40.04        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO 
       41.46        28.77        53.06        45.86        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX 
       71.34         8.98        53.36        60.99        62.37        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
       28.34        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       37.94        36.43        22.59        19.17         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                         1.02                          0.72 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                       113.98                        165.17 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                       25.680                        26.825 
[1] "1.0 - 114.0 (25.7)" "0.7 - 165.2 (26.8)"
[1] "hr=" "1.6"
D42V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 14(6P25.1) MUTATED    10  28   3
  DEL PEAK 14(6P25.1) WILD-TYPE 178 253   7
D42V3, multiclass
    clus
vv   DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  T2                          10                           178
  T3                          28                           253
  T4                           3                             7
[1] 3 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    26  14
  DEL PEAK 14(6P25.1) WILD-TYPE 312  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(6P25.1) MUTATED     26   14
  DEL PEAK 14(6P25.1) WILD-TYPE  312   61
   clus
vv  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  0                          26                           312
  1                          14                            61
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(6P25.1) MUTATED     1  40
  DEL PEAK 14(6P25.1) WILD-TYPE  13 428
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(6P25.1) MUTATED      1   40
  DEL PEAK 14(6P25.1) WILD-TYPE   13  428
                                        clus
vv                                       DEL PEAK 14(6P25.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             40
                                        clus
vv                                       DEL PEAK 14(6P25.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              428
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(6P25.1) MUTATED    24  15   0   1
  DEL PEAK 14(6P25.1) WILD-TYPE 286 123   5  14
D42V6, multiclass
    clus
vv   DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  R0                          24                           286
  R1                          15                           123
  R2                           0                             5
  RX                           1                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   169   4
  DEL PEAK 15(6Q14.3) WILD-TYPE 304   4
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          173                           308 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                            4                             4 
$`DEL PEAK 15(6Q14.3) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5748 
       32.71        33.96         3.68        11.51         2.99         1.02 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5767 
       35.01         1.02         2.04         0.92         1.02        15.06 
TCGA-CH-5788 TCGA-CH-5792 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5507 TCGA-EJ-5509 
       26.99         2.99        28.93        30.31        23.90        48.13 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       48.53        36.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 
       41.85        88.34        74.10        83.57        36.13        25.35 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7788 
        6.28        24.39        38.37        25.68        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65E 
       18.15        77.16        38.10        25.74        12.92        13.71 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI 
       14.83         7.56        10.82         8.75        15.42        13.45 
TCGA-FC-A5OB TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6362 
       22.36        81.04        66.67        46.16        46.52        47.44 
TCGA-G9-6379 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-A9S0 
       58.45        56.75        64.18        50.73        38.96        26.01 
TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7213 TCGA-HC-7736 
        3.68        65.26        36.36        28.54        40.08         0.72 
TCGA-HC-7747 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8261 TCGA-HC-8262 
       24.59        31.43        28.27        23.87        17.95        22.32 
TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO 
        1.58        22.36         0.76         2.01         2.20        17.42 
TCGA-HC-A6AP TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
        2.33        22.88        13.87        10.62        13.32        40.67 
TCGA-J9-A8CP TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z 
       12.69        21.86         8.65        19.66        56.28        86.40 
TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AV TCGA-KK-A7B0 TCGA-KK-A8I4 
       54.54        49.25        58.19        27.02        32.84        67.99 
TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ 
       32.91         2.73        67.43        82.36       113.98        51.25 
TCGA-KK-A8IK TCGA-M7-A71Z TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL 
       51.39        21.14        13.15        34.85        29.23         3.19 
TCGA-QU-A6IO TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A9O5 
      122.17        13.32        28.18        39.29        53.16        58.39 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9Z9 
       38.93        41.19        12.20        15.65         8.42        17.75 
TCGA-V1-A9ZG TCGA-VN-A88O TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 
       49.87        15.81        25.78       111.39        75.91        97.41 
TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS 
       85.18        21.80        42.94        44.88        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XK-AAIR 
        3.91        37.05        38.04        42.08        48.03        31.96 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        41.49        30.58        41.39        36.95        47.15 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       32.19        25.48        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8SH TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ 
       62.14        28.77        46.29        32.45       114.38        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW 
        8.98        14.04        53.36        60.99        62.37         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       14.53        13.28        11.67        29.85        22.59        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.43        16.96        17.98        11.47        13.48 

$`DEL PEAK 15(6Q14.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       20.42        43.79        22.06        25.35        31.96        30.31 
TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
       20.22         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5762 TCGA-CH-5763 
        1.97        24.03        13.02        31.00        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        23.01        24.03         2.04        13.02        15.98 
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-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       45.73        27.19        38.93        36.69        38.53        60.23 
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-7125 TCGA-EJ-7314 TCGA-EJ-7315 
       60.23        47.87        29.06        93.70        37.81        33.14 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 
       33.83        27.09        35.18        30.35        27.68        23.90 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       25.87        20.55        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       19.92        76.41        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65F 
       17.23        21.96        23.80        21.96        23.34        18.41 
TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU 
        6.48        15.65         4.21         9.27         9.83         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.31         4.77        28.41        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       41.62        87.35        67.99        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6363 
       68.68        49.81        50.70        49.35        47.15        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-G9-6384 TCGA-G9-6385 
       40.31        26.66        31.50        37.97        25.15        27.29 
TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       58.22        52.93        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7079 
       32.68        23.93         6.08        30.94        19.76         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       37.35        14.47         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        1.68        23.70        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A631 
        2.17         2.27        22.55        15.88         1.15         1.78 
TCGA-HC-A6AN TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        1.61         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K 
        6.02        25.28        27.91        16.83        22.52        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       23.67        14.37        20.28        11.77        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A8CM TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
        5.85        15.22        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY 
       43.66         8.88        11.57       113.10        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 
       30.02       165.17        67.59       115.13       113.33        67.07 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
        6.44        52.93        58.36        34.65        51.68        49.94 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        20.94       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       65.82        31.79        63.48        69.27        26.43        66.18 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A723 TCGA-M7-A725 
       20.65        47.28         5.19        12.62        25.08        18.84 
TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        5.69        41.00       140.19        86.14        18.12        11.90 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8WL TCGA-V1-A8WN 
       41.23        40.44        16.70        14.73        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       15.58        22.55         6.64        79.73         6.71        20.91 
TCGA-V1-A9OL TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-V1-A9ZR 
       19.36         5.59         4.27         6.15         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P 
        8.84        25.51        24.53         6.21        15.52        41.42 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D 
       44.91        16.31       109.58        23.93        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-WW-A8ZI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       66.97        53.36        14.76         9.04         2.99        31.99 
TCGA-XK-AAIW TCGA-XK-AAJU TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8S9 TCGA-YL-A8SA 
       40.04        51.81         4.87        52.96        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SP 
       56.52        41.46        45.14        53.06        45.86        71.34 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L2 
       24.33        49.91        28.34        10.13         4.27        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       36.43        20.28         3.78        19.04        12.16        22.75 
TCGA-ZG-A9MC TCGA-ZG-A9NI 
       14.96         4.34 

  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                         0.72                          0.79 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                       122.17                        165.17 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                        30.31                         25.30 
[1] "0.7 - 122.2 (30.3)" "0.8 - 165.2 (25.3)"
[1] "hr=" "1.6"
D43V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 15(6Q14.3) MUTATED    57 111   5
  DEL PEAK 15(6Q14.3) WILD-TYPE 131 170   5
D43V3, multiclass
    clus
vv   DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  T2                          57                           131
  T3                         111                           170
  T4                           5                             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"
D43V4, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q14.3) MUTATED   117  37
  DEL PEAK 15(6Q14.3) WILD-TYPE 221  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q14.3) MUTATED    117   37
  DEL PEAK 15(6Q14.3) WILD-TYPE  221   38
   clus
vv  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  0                         117                           221
  1                          37                            38
[1] 2 2
[1] FALSE
D43V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q14.3) MUTATED     5 168
  DEL PEAK 15(6Q14.3) WILD-TYPE   9 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q14.3) MUTATED      5  168
  DEL PEAK 15(6Q14.3) WILD-TYPE    9  300
                                        clus
vv                                       DEL PEAK 15(6Q14.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            168
                                        clus
vv                                       DEL PEAK 15(6Q14.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              300
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6Q14.3) MUTATED    91  63   2  10
  DEL PEAK 15(6Q14.3) WILD-TYPE 219  75   3   5
D43V6, multiclass
    clus
vv   DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  R0                          91                           219
  R1                          63                            75
  R2                           2                             3
  RX                          10                             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"
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    27   1
  DEL PEAK 16(7Q31.33) WILD-TYPE 446   7
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            28                            453 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                             1                              7 
$`DEL PEAK 16(7Q31.33) MUTATED`
TCGA-4L-AA1F TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5521 TCGA-EJ-7123 TCGA-G9-6366 
       11.51         0.92        26.99        51.88        74.10         3.32 
TCGA-HC-7080 TCGA-HC-7821 TCGA-HC-A6AO TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-AATZ 
       36.36        31.43        17.42        22.52        22.88        13.55 
TCGA-KK-A59V TCGA-KK-A6E4 TCGA-KK-A8IB TCGA-KK-A8IH TCGA-QU-A6IO TCGA-VN-A88L 
      113.10       115.13         2.73        66.18       122.17        24.53 
TCGA-VP-A87B TCGA-VP-A87D TCGA-XK-AAIV TCGA-XK-AAJA TCGA-YL-A8S9 TCGA-YL-A8SL 
       85.18        60.92        37.25        30.58        60.56        32.45 
TCGA-YL-A8SO TCGA-YL-A9WI TCGA-ZG-A8QZ TCGA-ZG-A9N3 
      114.38        53.36        10.13        11.47 

$`DEL PEAK 16(7Q31.33) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 
       25.35        31.96        30.31        20.22         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-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-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-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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        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-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-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       88.34        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        13.45        22.36        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        83.87        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-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        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        58.45        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        64.18        50.73        52.93 
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        23.93         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 
       65.26         2.93        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        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-A6AP TCGA-HC-A6AQ 
        1.78         2.01         2.20         1.61         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       27.91        16.83        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       11.77        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
       54.54       165.17        67.59        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP 
       18.84         5.69         3.19        41.00       140.19        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N 
        4.70         5.82         8.84        25.51         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E 
       75.91       109.58        97.41        23.93        55.56        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        53.36        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.99        31.96        40.04        41.49 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       53.06        45.86        46.29        71.34        62.79         8.98 
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-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        13.48         4.34 

  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                          0.92                           0.72 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                        122.17                         165.17 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                         31.94                          26.04 
[1] "0.9 - 122.2 (31.9)" "0.7 - 165.2 (26.0)"
[1] "hr=" "1.5"
D44V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 16(7Q31.33) MUTATED     8  20   0
  DEL PEAK 16(7Q31.33) WILD-TYPE 180 261  10
D44V3, multiclass
    clus
vv   DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  T2                            8                            180
  T3                           20                            261
  T4                            0                             10
[1] 3 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    17   8
  DEL PEAK 16(7Q31.33) WILD-TYPE 321  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(7Q31.33) MUTATED     17    8
  DEL PEAK 16(7Q31.33) WILD-TYPE  321   67
   clus
vv  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  0                           17                            321
  1                            8                             67
[1] 2 2
[1] FALSE
D44V5, binary
                                cls
clus                               0   1
  DEL PEAK 16(7Q31.33) MUTATED     0  28
  DEL PEAK 16(7Q31.33) WILD-TYPE  14 440
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(7Q31.33) MUTATED      0   28
  DEL PEAK 16(7Q31.33) WILD-TYPE   14  440
                                        clus
vv                                       DEL PEAK 16(7Q31.33) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              28
                                        clus
vv                                       DEL PEAK 16(7Q31.33) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               440
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(7Q31.33) MUTATED    18   9   0   0
  DEL PEAK 16(7Q31.33) WILD-TYPE 292 129   5  15
D44V6, multiclass
    clus
vv   DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  R0                           18                            292
  R1                            9                            129
  R2                            0                              5
  RX                            0                             15
[1] 4 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   213   4
  DEL PEAK 17(8P23.2) WILD-TYPE 260   4
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          217                           264 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                            4                             4 
$`DEL PEAK 17(8P23.2) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYO 
       32.71        22.06        33.96         3.68        25.35        30.31 
TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5753 
       20.22        11.51        22.06         1.97        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92         1.02        23.01         1.02        15.06 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5507 
       13.02        26.99        33.01        46.52        44.88        23.90 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5524 
       36.69        48.53        52.27        64.50        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       36.66        38.76        60.23        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7314 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7781 
       74.10        37.81        27.09        35.18        27.68        23.90 
TCGA-EJ-7783 TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46I 
       25.87        76.41        24.85        25.18        25.74        21.96 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A8FS TCGA-EJ-AB27 TCGA-FC-7708 
       12.92        13.71        18.41         8.75         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6339 TCGA-G9-6342 
       15.42        13.45        87.35        81.04        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 
       18.21        49.35        46.52        45.30        39.39         3.32 
TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 
       39.95        40.31        26.66        31.50        25.15        58.22 
TCGA-G9-6496 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 
       56.75        52.93        38.96        30.97        35.34        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 
       23.93         6.08        65.26        37.35        40.08         2.37 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7752 TCGA-HC-7819 TCGA-HC-7821 
        1.48         1.68        23.70        25.71        17.85        31.43 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       22.42        28.27        23.87        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO 
        1.15        22.36         0.76         2.01         2.20        17.42 
TCGA-HC-A6AQ TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 
        3.48         9.53        78.61        82.92        43.69        12.30 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A83I TCGA-J4-A83L 
       30.94        16.54        27.39         6.02        22.52        23.67 
TCGA-J4-A83N TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.55        10.62        13.32        15.22        40.67 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A6E1 
        8.65        19.66         8.88        11.57        44.68        54.54 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       49.94        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ 
       31.79        32.91        63.48        82.36       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       51.39        47.28        21.14        18.84         5.69         3.19 
TCGA-QU-A6IO TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
      122.17        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       40.44        39.29        52.08        15.58        22.55         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 
       79.73         6.71        20.91        41.19        19.36         4.27 
TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VP-A875 
        4.70        25.51         6.21        15.81        41.42        75.91 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-XJ-A83F 
       85.18        55.56        60.92        53.36        42.94        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       38.04        42.08        48.03         2.99        31.96        37.25 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YJ-A8SW TCGA-YL-A8HK 
       41.49        30.58        41.39        36.95         4.87        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        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       71.34         8.98        14.04        60.99        62.37        24.33 
TCGA-ZG-A9KY TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS 
        4.27        22.59        20.28        19.17        12.43        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

$`DEL PEAK 17(8P23.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-AAYF TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 
       20.42        43.79        31.96         2.99         6.97         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       12.99        13.97        24.03         1.02        13.02        31.00 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 
       44.02        12.00        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-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       13.32        29.79        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       27.19        38.93        48.13        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5522 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7125 
       46.55        47.80        68.35        39.75        41.85        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7327 
       83.57        36.13        33.14        25.35        33.83        30.35 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28        24.39        38.37        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-8470 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       19.92        77.16        38.10        21.60        20.58        17.23 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A65B TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       21.96        23.80        23.34        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU 
       15.65         4.21        10.82         9.27         9.83         4.54 
TCGA-EJ-AB20 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
        4.31        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       67.99        66.67        68.68        49.81        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 
       47.15        47.44        44.81        40.18        38.01        37.97 
TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7523 
       58.45        27.29        64.18        50.73        27.91        28.18 
TCGA-G9-7525 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
       32.68        30.94         3.68        19.76         2.93        36.36 
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        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7747 
       44.55         0.72         2.10        31.69        23.57        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
       26.04         1.97        17.16        30.51        30.84        24.56 
TCGA-HC-8213 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-A631 
       19.36         2.17         2.27        22.55        17.95         1.78 
TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        1.61         2.33         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-A67K 
        4.93        25.48        18.84        88.24        20.19        33.01 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A6G3 
       25.32        27.58        32.05        29.92        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AAU2 
       16.83        22.88        10.78        14.37        11.77        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.87         5.85        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       44.35        43.66        21.86       113.10        56.28        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      115.86        30.02       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        51.68        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       29.56         2.73        67.43        69.27        26.43        66.18 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       20.65         5.19        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-V1-A8MK TCGA-V1-A8ML 
       29.23        41.00       140.19        86.14        16.70        14.73 
TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A9O5 TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT 
       53.16        30.38        58.39        38.93        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR 
        8.42         5.59         6.15        17.75        49.87         5.82 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        8.84        24.53        15.52        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87E TCGA-VP-A87H 
      111.39       109.58        97.41        23.93        66.97        21.80 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DK 
       44.88        14.76        45.47        32.19         3.91         9.04 
TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       31.99        40.04        47.15        51.81        32.19        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA 
       52.96        51.45        48.72        71.77        62.14        16.83 
TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WI 
       56.52        28.77        53.06        32.45        62.79        53.36 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9LN TCGA-ZG-A9LZ 
       11.67        37.94        36.43        29.85         3.78        22.75 

  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                         0.76                          0.72 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       122.17                        165.17 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       26.990                        26.365 
[1] "0.8 - 122.2 (27.0)" "0.7 - 165.2 (26.4)"
[1] "hr=" "1.4"
D45V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 17(8P23.2) MUTATED    57 155   6
  DEL PEAK 17(8P23.2) WILD-TYPE 131 126   4
D45V3, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  T2                          57                           131
  T3                         155                           126
  T4                           6                             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"
D45V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED   146  45
  DEL PEAK 17(8P23.2) WILD-TYPE 192  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED    146   45
  DEL PEAK 17(8P23.2) WILD-TYPE  192   30
   clus
vv  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  0                         146                           192
  1                          45                            30
[1] 2 2
[1] FALSE
D45V5, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED     6 212
  DEL PEAK 17(8P23.2) WILD-TYPE   8 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED      6  212
  DEL PEAK 17(8P23.2) WILD-TYPE    8  256
                                        clus
vv                                       DEL PEAK 17(8P23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            212
                                        clus
vv                                       DEL PEAK 17(8P23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              256
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(8P23.2) MUTATED   135  67   3   9
  DEL PEAK 17(8P23.2) WILD-TYPE 175  71   2   6
D45V6, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  R0                         135                           175
  R1                          67                            71
  R2                           3                             2
  RX                           9                             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   279   6
  DEL PEAK 18(8P21.3) WILD-TYPE 194   2
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          285                           196 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                            6                             2 
$`DEL PEAK 18(8P21.3) MUTATED`
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       43.79        32.71        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5741 
       31.96        30.31        20.22        11.51        22.06        12.99 
TCGA-CH-5744 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.97        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        44.02         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       24.03        13.02        26.99        32.02        33.01         2.99 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5504 
       33.11        19.56        13.32        46.52        44.88        28.93 
TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5517 TCGA-EJ-5518 
       23.90        36.69        48.53        38.53        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        51.88        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        88.34        74.10 
TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7330 
       37.81        33.83        27.09        35.18        27.68         6.28 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7797 TCGA-EJ-8469 
       23.90        25.87        14.14        18.15        19.92        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       38.10        24.85        25.18        12.92        13.71        18.41 
TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A8FS TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        7.56        15.58         8.75         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       13.45        87.35        81.04        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       18.21        49.35        46.52        47.44        45.30        39.39 
TCGA-G9-6366 TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 
        3.32        39.95        40.31        26.66        31.50        58.45 
TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 
       25.15        58.22        56.75        52.93        38.96        30.97 
TCGA-G9-7522 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7081 
       35.34        26.01        23.93         6.08        65.26        37.35 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7742 TCGA-HC-7744 
        0.79        28.60        40.08         2.37         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7819 
       23.70        24.59        26.04         1.97        25.71        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8262 
       24.56        31.43        22.42        28.27        23.87        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-A6AQ TCGA-HC-A6AS TCGA-HC-A8CY 
        2.20         1.61        17.42         3.48         1.45         9.53 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67M 
       78.61        82.92        43.69        20.19        12.30        30.94 
TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A83I TCGA-J4-A83L TCGA-J4-A83N 
       16.54        27.39         6.02        22.52        23.67        20.28 
TCGA-J4-AATZ TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.55        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KK-A59Y TCGA-KK-A6DY 
       43.66         8.65        19.66         8.88        44.68       115.86 
TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       54.54       115.13        49.25        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B3 
       58.36        27.02        34.65        49.94        32.84        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 
      113.98        51.25        51.39        47.28        21.14        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-SU-A7E7 TCGA-TP-A8TT 
        5.69         3.19       140.19       122.17        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MM TCGA-V1-A8WL 
       13.32        41.23        28.18        40.44        39.29        52.08 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       15.58        22.55         6.64        79.73         6.71        20.91 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZI TCGA-V1-A9ZR 
       41.19        19.36         4.27         6.15         4.70         5.82 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       25.51         6.21        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       16.31        75.91        97.41        85.18        55.56        60.92 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       53.36        42.94        44.88        37.05        38.04        42.08 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
        2.99        31.96        37.25        41.49        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       47.15        32.19         4.87        49.02        51.45        48.72 
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-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       45.86        46.29        32.45       114.38        71.34         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
       28.34        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

$`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 
       93.70        83.57        36.13        33.14        25.35        30.35 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7791 
       24.39        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        77.16        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.54         4.31        22.36        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 
       64.18        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        36.36        14.47        28.54 
TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        1.68        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-8213 TCGA-HC-8258 
       23.57        17.16        30.51        30.84        19.36         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A6HX 
        2.27        22.55        17.95         1.78         2.33         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        4.41         7.00         4.93        25.48        18.84        88.24 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A6G1 
       33.01        25.32        27.58        32.05        29.92        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV 
       27.91        16.83        22.88        10.78        14.37        11.77 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       27.12        13.87         5.85        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       44.35        21.86        11.57       113.10        56.28        86.40 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AY 
       30.02       165.17        67.59       113.33        67.07        51.68 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IH TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        36.13         2.73        66.18        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IM 
       12.62        13.15        34.85        25.08        29.23        41.00 
TCGA-QU-A6IP TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A9O5 
       86.14        16.70        14.73        53.16        30.38        58.39 
TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 
       38.93        12.20        15.65         8.42         5.59        17.75 
TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88N TCGA-VP-A872 TCGA-VP-A876 
       49.87         8.84        24.53        15.52       111.39       109.58 
TCGA-VP-A879 TCGA-VP-A87E TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       23.93        66.97        21.80        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJA 
        3.91        48.03         9.04        31.99        40.04        30.58 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI 
       51.81        25.48        52.96        71.77        56.52        53.06 
TCGA-YL-A8SQ TCGA-ZG-A8QW TCGA-ZG-A9L4 TCGA-ZG-A9LN 
       62.79         3.09        36.43         3.78 

  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                         0.76                          0.72 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                       140.19                        165.17 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                       28.180                        25.335 
[1] "0.8 - 140.2 (28.2)" "0.7 - 165.2 (25.3)"
[1] "hr=" "1.5"
D46V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 18(8P21.3) MUTATED    81 197   8
  DEL PEAK 18(8P21.3) WILD-TYPE 107  84   2
D46V3, multiclass
    clus
vv   DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  T2                          81                           107
  T3                         197                            84
  T4                           8                             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"
D46V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P21.3) MUTATED   195  58
  DEL PEAK 18(8P21.3) WILD-TYPE 143  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P21.3) MUTATED    195   58
  DEL PEAK 18(8P21.3) WILD-TYPE  143   17
   clus
vv  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  0                         195                           143
  1                          58                            17
[1] 2 2
[1] FALSE
D46V5, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P21.3) MUTATED     7 279
  DEL PEAK 18(8P21.3) WILD-TYPE   7 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P21.3) MUTATED      7  279
  DEL PEAK 18(8P21.3) WILD-TYPE    7  189
                                        clus
vv                                       DEL PEAK 18(8P21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           7
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            279
                                        clus
vv                                       DEL PEAK 18(8P21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             7
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              189
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P21.3) MUTATED   172  92   3  10
  DEL PEAK 18(8P21.3) WILD-TYPE 138  46   2   5
D46V6, multiclass
    clus
vv   DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  R0                         172                           138
  R1                          92                            46
  R2                           3                             2
  RX                          10                             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    43   0
  DEL PEAK 19(9P23) WILD-TYPE 430   8
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         43                         438 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                          0                           8 
$`DEL PEAK 19(9P23) MUTATED`
TCGA-2A-A8VX TCGA-4L-AA1F TCGA-CH-5746 TCGA-CH-5751 TCGA-CH-5766 TCGA-EJ-5507 
       33.96        11.51        24.03        35.01         1.02        23.90 
TCGA-EJ-5509 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-7781 TCGA-EJ-7784 
       48.13        47.80        64.50        51.88        23.90        25.68 
TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6377 TCGA-G9-7521 TCGA-HC-7213 
       14.14        15.42        13.45        31.50        30.97        40.08 
TCGA-HC-8216 TCGA-HC-A631 TCGA-HI-7168 TCGA-J4-A67L TCGA-J4-A83J TCGA-J9-A52E 
       22.42         1.78        78.61        25.32        22.88        10.62 
TCGA-KC-A7F6 TCGA-KK-A6DY TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8IH TCGA-M7-A725 
        8.65       115.86        31.79        67.43        66.18        18.84 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-VP-A87D TCGA-XJ-A83F TCGA-XK-AAIV 
       15.58        22.55        58.39        60.92        37.05        37.25 
TCGA-XK-AAJA TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A9WH TCGA-YL-A9WY 
       30.58         4.87        62.14        56.52        14.04        28.34 
TCGA-ZG-A9LY 
       12.16 

$`DEL PEAK 19(9P23) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 
        1.02        12.99        13.97         1.97         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
        1.02        23.01        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-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       27.19        38.93        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       60.23        46.55        52.27        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 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
       27.68         6.28        24.39        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-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6378 
       40.18        39.95        38.01        40.31        26.66        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        52.93        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        23.93         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        65.26         2.93        36.36        37.35        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        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
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-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       20.19        12.30        33.01        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.52        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CL 
       11.77        13.55        27.12        13.87         5.85        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       44.35        43.66        21.86        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        56.28        44.68        86.40        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 
       20.94        67.99       101.79        21.96        65.82        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II 
       63.48         2.73        69.27        26.43        82.36       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC 
       12.62        13.15        34.85        25.08        29.23         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       11.90        13.32        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8X3 
       14.73        39.29        53.16        52.08        30.38         6.64 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        85.18        55.56        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19         3.91 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        40.04        41.49        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       51.81        32.19        25.48        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       48.72        71.77        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        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         8.98        53.36        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                       1.02                        0.72 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                     115.86                      165.17 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                     28.340                      26.545 
[1] "1.0 - 115.9 (28.3)" "0.7 - 165.2 (26.5)"
[1] "hr="     "8.2e+07"
D47V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK 19(9P23) MUTATED    10  31   2
  DEL PEAK 19(9P23) WILD-TYPE 178 250   8
D47V3, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  T2                        10                         178
  T3                        31                         250
  T4                         2                           8
[1] 3 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    29  12
  DEL PEAK 19(9P23) WILD-TYPE 309  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     29   12
  DEL PEAK 19(9P23) WILD-TYPE  309   63
   clus
vv  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  0                        29                         309
  1                        12                          63
[1] 2 2
[1] FALSE
D47V5, binary
                             cls
clus                            0   1
  DEL PEAK 19(9P23) MUTATED     1  42
  DEL PEAK 19(9P23) WILD-TYPE  13 426
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED      1   42
  DEL PEAK 19(9P23) WILD-TYPE   13  426
                                        clus
vv                                       DEL PEAK 19(9P23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           42
                                        clus
vv                                       DEL PEAK 19(9P23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            426
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(9P23) MUTATED    24  17   0   1
  DEL PEAK 19(9P23) WILD-TYPE 286 121   5  14
D47V6, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  R0                        24                         286
  R1                        17                         121
  R2                         0                           5
  RX                         1                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   149   2
  DEL PEAK 20(10Q23.31) WILD-TYPE 324   6
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            151                             330 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                              2                               6 
$`DEL PEAK 20(10Q23.31) MUTATED`
TCGA-2A-A8VT TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 
       32.71        20.22        11.51         2.99         1.02        12.99 
TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5766 TCGA-CH-5769 TCGA-CH-5790 
        1.97        35.01         2.04         1.02         2.04        32.02 
TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5504 
       33.01        29.00        33.11        46.52        44.88        28.93 
TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 
       23.90        36.69        36.23        46.55        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-EJ-7312 
       51.88        68.35        43.07        39.75        29.06        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7327 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8469 
       37.81        33.14        30.35        25.68        14.14        76.41 
TCGA-EJ-A46F TCGA-EJ-A65J TCGA-EJ-A7NM TCGA-FC-7708 TCGA-FC-7961 TCGA-G9-6332 
       25.74        14.83         4.21        28.41        15.42        87.35 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 
       83.87        55.76        49.81        47.15        46.52        45.30 
TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7522 
       39.39        26.66        31.50        50.73        30.97        35.34 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 
       32.68        23.93        37.35        14.47        28.54        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-7742 
       40.08         1.68         2.37        38.17         2.10         1.48 
TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
        1.68        26.04         1.97        15.88         1.15        22.36 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A8D0 TCGA-HI-7168 TCGA-HI-7171 
        1.78         2.20         1.61        25.48        78.61        43.69 
TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-AATZ TCGA-J9-A52B 
       16.54        27.39        22.52        22.88        13.55        13.87 
TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7FA TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       15.22        43.66        19.66        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU 
       30.02        54.54       113.33        67.07        52.93        58.36 
TCGA-KK-A7AY TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IA 
       51.68        29.56        20.94       101.79        21.96        63.48 
TCGA-KK-A8IC TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IM TCGA-M7-A721 TCGA-MG-AAMC 
       67.43        66.18       113.98        47.28        13.15         5.69 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MJ TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OL 
       18.12        11.90        40.44        58.39         6.71        19.36 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-VN-A88L TCGA-VN-A88Q 
        4.27         6.15        17.75        49.87        24.53        44.91 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XJ-A83F 
      111.39        75.91        53.36        42.94        44.88        37.05 
TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA 
       48.03        37.25        47.15        49.02        51.45        16.83 
TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WL 
       45.14        45.86        32.45        14.04        62.37        24.33 
TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       28.34        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       20.28        12.43        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 
       11.47 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5743 TCGA-CH-5746 
       31.96        30.31         6.97        22.06        13.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        31.00         1.02         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 
       12.00         1.02        23.01        15.06        24.03        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5496 
       15.98        26.99         9.99         2.99        27.16        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       13.32        29.79        26.30        45.73        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 
       38.93        48.13        48.53        38.53        60.23        47.80 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       36.66        38.76        60.23        41.85        47.87        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       74.10        93.70        83.57        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       35.18        27.68         6.28        24.39        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-8470 TCGA-EJ-8472 
        3.75        23.05        19.92        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       25.18        21.60        20.58        17.23        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        6.48        15.65        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54         4.31         4.77        13.45        22.36        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-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6362 
       18.21        68.68        46.16        50.70        49.35        47.44 
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-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7523 TCGA-G9-A9S0 
       64.18        52.93        38.96        27.91        28.18        26.01 
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        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7211 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 TCGA-HC-7740 
       36.36         0.79        44.55         0.72        31.69        23.57 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       23.70        24.59        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.58         0.76         2.01        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       18.84        88.24        82.92        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T 
       25.32        30.94        27.58        32.05        29.92         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       25.28        27.91        16.83        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        11.77        27.12         5.85        10.62        13.32 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
       21.86         8.65         8.88        11.57       113.10        56.28 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AP 
      165.17        67.59       115.13        49.25        58.19         6.44 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        34.65        49.94        32.84        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID 
       67.99        65.82        31.79        32.91         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       26.43        82.36        51.25        51.39        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       21.14        12.62        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TV 
        3.19        41.00       140.19       122.17        86.14        13.32 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       41.23        28.18        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O7 
       52.08        30.38        15.58        22.55         6.64        79.73 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        41.19        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M 
        5.59         4.70         5.82         8.84        25.51         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.52        15.81        41.42        25.78        16.31       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        14.76        45.47        32.19         3.91        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       42.08         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       41.49        30.58        41.39        36.95        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48         4.87        52.96        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       60.56        56.52        41.46        28.77        53.06        46.29 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34        62.79         8.98        53.36        60.99 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       49.91         3.09        14.53        13.28        29.85        22.59 
TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.17         3.78        16.96        19.04        13.48         4.34 

  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                           1.02                            0.72 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         115.86                          165.17 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                          30.35                           25.30 
[1] "1.0 - 115.9 (30.4)" "0.7 - 165.2 (25.3)"
[1] "hr=" "1.5"
D48V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 20(10Q23.31) MUTATED    37 109   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 151 172   4
D48V3, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  T2                            37                             151
  T3                           109                             172
  T4                             6                               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"
D48V4, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED   107  38
  DEL PEAK 20(10Q23.31) WILD-TYPE 231  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED    107   38
  DEL PEAK 20(10Q23.31) WILD-TYPE  231   37
   clus
vv  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  0                           107                             231
  1                            38                              37
[1] 2 2
[1] FALSE
D48V5, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED     5 147
  DEL PEAK 20(10Q23.31) WILD-TYPE   9 321
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED      5  147
  DEL PEAK 20(10Q23.31) WILD-TYPE    9  321
                                        clus
vv                                       DEL PEAK 20(10Q23.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              147
                                        clus
vv                                       DEL PEAK 20(10Q23.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                               9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                321
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 20(10Q23.31) MUTATED    89  53   2   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 221  85   3   9
D48V6, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  R0                            89                             221
  R1                            53                              85
  R2                             2                               3
  RX                             6                               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"
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    33   1
  DEL PEAK 21(11P11.2) WILD-TYPE 440   7
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            34                            447 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                             1                              7 
$`DEL PEAK 21(11P11.2) MUTATED`
TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5788 TCGA-EJ-5531 TCGA-EJ-7789 TCGA-EJ-8472 
        3.68        11.51        26.99        41.85        18.15        24.85 
TCGA-FC-7708 TCGA-G9-6379 TCGA-HC-7737 TCGA-HI-7171 TCGA-J4-A83J TCGA-J9-A52C 
       28.41        58.45         2.10        43.69        22.88         5.85 
TCGA-J9-A8CL TCGA-KK-A59X TCGA-KK-A7AU TCGA-KK-A8IB TCGA-KK-A8IG TCGA-KK-A8IK 
       13.32        56.28        58.36         2.73        82.36        51.39 
TCGA-QU-A6IM TCGA-V1-A8MG TCGA-V1-A9Z7 TCGA-VN-A88O TCGA-VP-AA1N TCGA-X4-A8KQ 
       41.00        28.18         4.27        15.81        44.88        45.47 
TCGA-XJ-A83G TCGA-XK-AAJP TCGA-XK-AAK1 TCGA-YL-A8S8 TCGA-YL-A8SL TCGA-YL-A8SQ 
       38.04        41.39        32.19        62.14        32.45        62.79 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A9KY TCGA-ZG-A9LZ 
       53.36        62.37         4.27        22.75 

$`DEL PEAK 21(11P11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06        33.96        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         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-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-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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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-5532 TCGA-EJ-5542 
       36.66        38.76        39.75        60.23        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        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        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        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        83.87 
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-G9-6384 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        64.18        50.73        52.93        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        23.93 
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        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        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 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
       25.48        18.84        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        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.52        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM 
       11.77        13.55        27.12        13.87        10.62        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19         6.44        52.93        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II 
       63.48        67.43        69.27        26.43        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        3.19       140.19       122.17        86.14        18.12        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       58.39        79.73         6.71        20.91        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 
       19.36        12.20        15.65         8.42         5.59         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53         6.21        15.52        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H 
       42.94        14.76        32.19         3.91        37.05        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        41.49        30.58        36.95        47.15        51.81 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       71.77        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29       114.38        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        8.98        14.04        60.99        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                          2.10                           0.72 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                         82.36                         165.17 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                         32.32                          26.01 
[1] "2.1 - 82.4 (32.3)"  "0.7 - 165.2 (26.0)"
[1] "hr=" "2.2"
D49V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 21(11P11.2) MUTATED     6  27   1
  DEL PEAK 21(11P11.2) WILD-TYPE 182 254   9
D49V3, multiclass
    clus
vv   DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  T2                            6                            182
  T3                           27                            254
  T4                            1                              9
[1] 3 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    24   7
  DEL PEAK 21(11P11.2) WILD-TYPE 314  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P11.2) MUTATED     24    7
  DEL PEAK 21(11P11.2) WILD-TYPE  314   68
   clus
vv  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  0                           24                            314
  1                            7                             68
[1] 2 2
[1] FALSE
D49V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P11.2) MUTATED     0  34
  DEL PEAK 21(11P11.2) WILD-TYPE  14 434
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P11.2) MUTATED      0   34
  DEL PEAK 21(11P11.2) WILD-TYPE   14  434
                                        clus
vv                                       DEL PEAK 21(11P11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              34
                                        clus
vv                                       DEL PEAK 21(11P11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               434
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(11P11.2) MUTATED    15  16   0   2
  DEL PEAK 21(11P11.2) WILD-TYPE 295 122   5  13
D49V6, multiclass
    clus
vv   DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  R0                           15                            295
  R1                           16                            122
  R2                            0                              5
  RX                            2                             13
[1] 4 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    43   0
  DEL PEAK 22(11Q22.3) WILD-TYPE 430   8
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            43                            438 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                             0                              8 
$`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        36.13         6.28        25.87        18.15        23.34 
TCGA-EJ-A7NM TCGA-FC-A4JI TCGA-G9-6494 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7232 
        4.21        13.45        58.22        28.54        28.60        38.17 
TCGA-HC-7736 TCGA-HC-7745 TCGA-HC-A76X TCGA-J9-A52C TCGA-J9-A8CL TCGA-KK-A59X 
        0.72        23.70         4.93         5.85        13.32        56.28 
TCGA-KK-A7AP TCGA-KK-A8I8 TCGA-KK-A8IK TCGA-SU-A7E7 TCGA-V1-A8MG TCGA-V1-A9OY 
        6.44        31.79        51.39        18.12        28.18         5.59 
TCGA-VP-AA1N TCGA-XJ-A9DX TCGA-XK-AAJR TCGA-XK-AAJT TCGA-YL-A8SK TCGA-YL-A8SO 
       44.88        31.99        36.95        47.15        46.29       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-ZG-A9KY TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       71.34        62.79         4.27        16.96        19.04        12.16 
TCGA-ZG-A9NI 
        4.34 

$`DEL PEAK 22(11Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-5754 
       24.03         1.02        13.02        35.01        31.00         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-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
       33.01        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-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        23.90        38.93        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-5530 
       51.88        68.35        43.07        36.66        38.76        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       35.18        30.35        27.68        24.39        23.90        38.37 
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        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       21.96        23.80        21.96        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FN TCGA-EJ-A8FO 
       14.20        15.58         6.48        15.65        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42        22.36        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        83.87        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-G9-6496 
       31.50        37.97        58.45        25.15        27.29        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        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        23.93         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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       37.35        14.47         0.79        40.08         1.68         2.37 
TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         2.10        31.69        23.57         1.48         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        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        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        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8CY 
        3.48         1.45         1.25         4.41         7.00         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.62        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57       113.10        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07        58.19        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM 
       82.36        66.18       113.98        51.25        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       29.23        18.84         5.69         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ 
      122.17        86.14        11.90        13.32        41.23        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        8.42         4.27         6.15        17.75        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        5.82         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        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        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
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        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.49        30.58        41.39        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        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        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SR TCGA-YL-A9WH 
       28.77        53.06        45.86        32.45         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 
        3.09        14.53        13.28        10.13        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
        3.78        22.75        17.98        14.96        11.47        13.48 

  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                          0.72                           0.76 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                        114.38                         165.17 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                        23.700                         27.005 
[1] "0.7 - 114.4 (23.7)" "0.8 - 165.2 (27.0)"
[1] "hr="     "7.7e+07"
D50V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 22(11Q22.3) MUTATED     7  33   3
  DEL PEAK 22(11Q22.3) WILD-TYPE 181 248   7
D50V3, multiclass
    clus
vv   DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  T2                            7                            181
  T3                           33                            248
  T4                            3                              7
[1] 3 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    26  10
  DEL PEAK 22(11Q22.3) WILD-TYPE 312  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q22.3) MUTATED     26   10
  DEL PEAK 22(11Q22.3) WILD-TYPE  312   65
   clus
vv  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  0                           26                            312
  1                           10                             65
[1] 2 2
[1] FALSE
D50V5, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q22.3) MUTATED     2  41
  DEL PEAK 22(11Q22.3) WILD-TYPE  12 427
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q22.3) MUTATED      2   41
  DEL PEAK 22(11Q22.3) WILD-TYPE   12  427
                                        clus
vv                                       DEL PEAK 22(11Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              41
                                        clus
vv                                       DEL PEAK 22(11Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               427
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(11Q22.3) MUTATED    18  23   0   0
  DEL PEAK 22(11Q22.3) WILD-TYPE 292 115   5  15
D50V6, multiclass
    clus
vv   DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  R0                           18                            292
  R1                           23                            115
  R2                            0                              5
  RX                            0                             15
[1] 4 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    47   0
  DEL PEAK 23(11Q23.2) WILD-TYPE 426   8
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            47                            434 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                             0                              8 
$`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        36.13         6.28        23.34        14.83        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-J9-A8CL 
       38.17         0.72        23.70         5.85        10.62        13.32 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E8 TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8IB 
       56.28        44.68        58.19       101.79        31.79         2.73 
TCGA-KK-A8IK TCGA-SU-A7E7 TCGA-V1-A8MG TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-V1-A9ZR 
       51.39        18.12        28.18         6.15        49.87         5.82 
TCGA-VP-AA1N TCGA-XJ-A9DX TCGA-XK-AAJR TCGA-XK-AAJT TCGA-YL-A8SK TCGA-YL-A8SP 
       44.88        31.99        36.95        47.15        46.29        71.34 
TCGA-YL-A8SQ TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9NI 
       62.79        16.96        19.04        22.75         4.34 

$`DEL PEAK 23(11Q23.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         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-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-5791 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
       33.01        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-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-5530 
       51.88        68.35        43.07        36.66        38.76        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       35.18        30.35        27.68        24.39        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        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.23        25.74        21.96        23.80        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        18.41        21.90         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.77        28.41        15.42        22.36        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 
       83.87        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-G9-6364 
       50.70        49.35        47.15        46.52        47.44        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-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 
       26.66        37.97        58.45        25.15        27.29        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        23.93         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        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 
       14.47         0.79        40.08         1.68         2.37        44.55 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        2.10        31.69        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        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        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       14.37        20.28        11.77        13.55        27.12        13.87 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       11.57       113.10        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       67.99        21.96        65.82        32.91        63.48        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       140.19       122.17        86.14        11.90        13.32 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       41.23        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       79.73         6.71        20.91        38.93        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z9 
       12.20        15.65         8.42         5.59         4.27        17.75 
TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        4.70         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        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        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
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        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.49        30.58        41.39        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        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        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SR 
       28.77        53.06        45.86        32.45       114.38         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        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-A9KY 
       28.34         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       11.67        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       19.17        12.43         3.78        12.16        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                          0.72                           0.76 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                        101.79                         165.17 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                        28.930                         26.025 
[1] "0.7 - 101.8 (28.9)" "0.8 - 165.2 (26.0)"
[1] "hr="     "7.8e+07"
D51V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 23(11Q23.2) MUTATED    11  33   4
  DEL PEAK 23(11Q23.2) WILD-TYPE 177 248   6
D51V3, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  T2                           11                            177
  T3                           33                            248
  T4                            4                              6
[1] 3 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    35   6
  DEL PEAK 23(11Q23.2) WILD-TYPE 303  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED     35    6
  DEL PEAK 23(11Q23.2) WILD-TYPE  303   69
   clus
vv  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  0                           35                            303
  1                            6                             69
[1] 2 2
[1] FALSE
D51V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     1  47
  DEL PEAK 23(11Q23.2) WILD-TYPE  13 421
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      1   47
  DEL PEAK 23(11Q23.2) WILD-TYPE   13  421
                                        clus
vv                                       DEL PEAK 23(11Q23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              47
                                        clus
vv                                       DEL PEAK 23(11Q23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               421
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11Q23.2) MUTATED    21  23   0   2
  DEL PEAK 23(11Q23.2) WILD-TYPE 289 115   5  13
D51V6, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  R0                           21                            289
  R1                           23                            115
  R2                            0                              5
  RX                            2                             13
[1] 4 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   119   3
  DEL PEAK 24(12P13.1) WILD-TYPE 354   5
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                           122                            359 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                             3                              5 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-2A-AAYU TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5751 
       32.71        25.35        20.22         1.97         1.02        35.01 
TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5792 TCGA-EJ-5501 
       31.00         0.92         1.02        24.03         2.99        44.88 
TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       23.90        36.69        36.23        52.27        64.50        68.35 
TCGA-EJ-5526 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7788 TCGA-EJ-7789 
       38.76        37.81        33.14        23.90        14.14        18.15 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       77.16        38.10        24.85        12.92        13.71        18.41 
TCGA-EJ-A7NH TCGA-EJ-A8FS TCGA-G9-6333 TCGA-G9-6354 TCGA-G9-6362 TCGA-G9-6364 
       15.58         8.75        81.04        49.35        47.44        39.39 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7525 TCGA-G9-A9S0 
       58.45        25.15        50.73        30.97        32.68        26.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7230 TCGA-HC-7736 TCGA-HC-7817 TCGA-HC-8216 
       37.35        14.47         1.68         0.72        30.51        22.42 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HI-7168 
       22.32         1.58        22.36         2.01         2.20        78.61 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A83J TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A8CP 
       30.94        16.54        22.88        13.55        13.87        12.69 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A6E1 TCGA-KK-A6E5 
       43.66        21.86        19.66        56.28        54.54        49.25 
TCGA-KK-A6E6 TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A8I4 
      113.33        34.65        49.94        34.95        29.56        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8II TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IO 
       67.43        82.36       113.98        18.84         5.69       122.17 
TCGA-V1-A8MF TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O9 TCGA-V1-A9OX TCGA-VN-A88R 
       41.23        15.58        22.55         6.71         8.42        25.78 
TCGA-VP-A872 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
      111.39        60.92        53.36        42.94        44.88        45.47 
TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       37.05        42.08        37.25        41.49        30.58        41.39 
TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SJ 
       47.15        51.45        48.72        16.83        41.46        45.86 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       60.99        62.37        28.34         4.27        11.67        37.94 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU 
       29.85        22.59        20.28        12.43        16.96        19.04 
TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       17.98        11.47 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF 
       20.42        43.79        22.06        33.96         3.68        31.96 
TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       30.31        11.51         2.99         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5754 
       12.99        13.97        24.03        13.02         1.02         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5769 
       44.02        12.00         1.02        23.01        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-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-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       47.80        51.88        43.07        36.66        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        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       83.57        36.13        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       25.68        20.55        14.53        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       23.05        19.92        76.41        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       14.20         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        9.83         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       87.35        67.99        66.67        83.87        55.76        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-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-6494 
       40.31        26.66        31.50        37.97        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       56.75        64.18        52.93        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       28.18        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       65.26         2.93        36.36        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 
       40.08         2.37        38.17        44.55         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.97        17.16        25.71        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       31.43        19.36        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.55        17.95        15.88         1.15         0.76         1.78 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
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        33.01 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       25.32        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       25.28        27.91        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       14.37        20.28        11.77        27.12         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        40.67        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y 
       44.35         8.65         8.88        11.57       113.10        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       86.40       115.86        30.02       165.17        67.59       115.13 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AY TCGA-KK-A7B0 TCGA-KK-A7B2 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-KK-A8ID 
       51.68        32.84        36.13        20.94         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       26.43        66.18        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 
       29.23         3.19        41.00       140.19        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       11.90        13.32        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8X3 TCGA-V1-A9O5 
       39.29        53.16        52.08        30.38         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       79.73        20.91        38.93        41.19        19.36        12.20 
TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       15.65         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 
       15.52        15.81        41.42        44.91        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E 
      109.58        97.41        23.93        85.18        55.56        66.97 
TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
       21.80        14.76        32.19         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJR 
        9.04         2.99        31.99        31.96        40.04        36.95 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       51.81        32.19        25.48         4.87        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        56.52        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       53.06        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
        8.98        14.04        53.36        24.33        49.91         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L4 TCGA-ZG-A9LB TCGA-ZG-A9LN 
       14.53        13.28        10.13        36.43        19.17         3.78 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        14.96        13.48         4.34 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          0.72                           0.76 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        122.17                         165.17 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        30.985                         25.680 
[1] "0.7 - 122.2 (31.0)" "0.8 - 165.2 (25.7)"
[1] "hr=" "1.6"
D52V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 24(12P13.1) MUTATED    23  94   5
  DEL PEAK 24(12P13.1) WILD-TYPE 165 187   5
D52V3, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  T2                           23                            165
  T3                           94                            187
  T4                            5                              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"
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    86  30
  DEL PEAK 24(12P13.1) WILD-TYPE 252  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     86   30
  DEL PEAK 24(12P13.1) WILD-TYPE  252   45
   clus
vv  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  0                           86                            252
  1                           30                             45
[1] 2 2
[1] FALSE
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED     6 116
  DEL PEAK 24(12P13.1) WILD-TYPE   8 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED      6  116
  DEL PEAK 24(12P13.1) WILD-TYPE    8  352
                                        clus
vv                                       DEL PEAK 24(12P13.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             116
                                        clus
vv                                       DEL PEAK 24(12P13.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               352
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(12P13.1) MUTATED    71  41   2   5
  DEL PEAK 24(12P13.1) WILD-TYPE 239  97   3  10
D52V6, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  R0                           71                            239
  R1                           41                             97
  R2                            2                              3
  RX                            5                             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"
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    41   1
  DEL PEAK 25(12Q24.32) WILD-TYPE 432   7
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             42                             439 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                              1                               7 
$`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 
       40.08         0.72         1.48        22.42        15.88         0.76 
TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BV TCGA-KC-A7FA 
       78.61        13.87        40.67        12.69        43.66        19.66 
TCGA-KK-A6E1 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IK 
       54.54        67.99        65.82        63.48        26.43        51.39 
TCGA-V1-A8MF TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-AA1N TCGA-XJ-A83G 
       41.23        25.51       111.39        75.91        44.88        38.04 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A9WJ TCGA-ZG-A8QY TCGA-ZG-A9L9 TCGA-ZG-A9M4 
       49.02        51.45        60.99        13.28        20.28        17.98 

$`DEL PEAK 25(12Q24.32) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       31.96        30.31        20.22        11.51         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-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-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-5509 
       45.73        28.93        30.31        27.19        23.90        48.13 
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-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 
       52.27        64.50        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        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       24.39        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-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        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        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       18.21        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-G9-6498 TCGA-G9-6499 
       37.97        58.45        25.15        27.29        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       52.93        38.96        27.91        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        23.93         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 
       65.26         2.93        36.36        37.35        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        38.17        44.55 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10        31.69        23.57         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        31.43        19.36        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
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 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       10.78        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A4BL 
       27.12         5.85        10.62        13.32        15.22        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       59.67        19.96        44.35        21.86         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       29.56        20.94       101.79        21.96        31.79        32.91 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
        2.73        67.43        69.27        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       11.90        13.32        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        58.39        79.73         6.71        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
        4.27         6.15        17.75        49.87         4.70         5.82 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       37.25        40.04        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       47.15        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       53.36        62.37        24.33        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                           0.72                            0.79 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                         111.39                          165.17 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                         38.845                          25.780 
[1] "0.7 - 111.4 (38.8)" "0.8 - 165.2 (25.8)"
[1] "hr=" "1.5"
D53V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 25(12Q24.32) MUTATED     7  34   1
  DEL PEAK 25(12Q24.32) WILD-TYPE 181 247   9
D53V3, multiclass
    clus
vv   DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  T2                             7                             181
  T3                            34                             247
  T4                             1                               9
[1] 3 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    27  12
  DEL PEAK 25(12Q24.32) WILD-TYPE 311  63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.32) MUTATED     27   12
  DEL PEAK 25(12Q24.32) WILD-TYPE  311   63
   clus
vv  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  0                            27                             311
  1                            12                              63
[1] 2 2
[1] FALSE
D53V5, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.32) MUTATED     1  41
  DEL PEAK 25(12Q24.32) WILD-TYPE  13 427
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.32) MUTATED      1   41
  DEL PEAK 25(12Q24.32) WILD-TYPE   13  427
                                        clus
vv                                       DEL PEAK 25(12Q24.32) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               41
                                        clus
vv                                       DEL PEAK 25(12Q24.32) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                427
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(12Q24.32) MUTATED    24  13   0   3
  DEL PEAK 25(12Q24.32) WILD-TYPE 286 125   5  12
D53V6, multiclass
    clus
vv   DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  R0                            24                             286
  R1                            13                             125
  R2                             0                               5
  RX                             3                              12
[1] 4 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   216   4
  DEL PEAK 26(13Q14.13) WILD-TYPE 257   4
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            220                             261 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                              4                               4 
$`DEL PEAK 26(13Q14.13) MUTATED`
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5740 
       31.96        30.31        11.51         2.99        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5748 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5764 
       12.99         1.02        31.00         2.04        44.02         1.02 
TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5792 
       23.01        24.03        13.02        15.98        26.99         2.99 
TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5499 TCGA-EJ-5504 TCGA-EJ-5507 
       29.00        33.11        19.56        46.52        28.93        23.90 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        36.23        46.55 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7115 
       52.27        51.88        36.66        39.75        41.85        88.34 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       74.10        83.57        33.14        25.35        33.83        27.09 
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-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       18.15        23.05        76.41        24.85        25.18        20.58 
TCGA-EJ-A65F TCGA-EJ-A65M TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-EJ-A8FS 
       18.41         7.56         8.22        15.58         4.21         8.75 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-G9-6329 TCGA-G9-6348 TCGA-G9-6361 TCGA-G9-6365 
       15.42        22.36        41.62        49.81        46.52        44.81 
TCGA-G9-6369 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 
       39.95        37.97        58.45        58.22        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7209 
       27.91        30.97         6.08        65.26        36.36        14.47 
TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7737 
       28.54        28.60        40.08         2.37        38.17         2.10 
TCGA-HC-7738 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7819 TCGA-HC-7821 
       31.69         1.68        24.59        17.16        17.85        31.43 
TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
       17.95         1.58         1.15        22.36         0.76         2.01 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HI-7168 TCGA-HI-7171 
        1.61        17.42         2.33         1.45        78.61        43.69 
TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67S TCGA-J4-A83I 
       20.19        33.01        25.32        30.94        27.39        22.52 
TCGA-J4-A83J TCGA-J4-A83M TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM 
       22.88        14.37        27.12        13.87        10.62        15.22 
TCGA-J9-A8CP TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       12.69        43.66        21.86        56.28        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 
      115.86        30.02        54.54       165.17       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AW TCGA-KK-A7B1 
      113.33        67.07        58.19         6.44        34.65        34.95 
TCGA-KK-A7B4 TCGA-KK-A8I6 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF 
       20.94        21.96        32.91        63.48         2.73        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A725 
       82.36        66.18       113.98        13.15        34.85        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
        3.19        41.00       122.17        11.90        13.32        41.23 
TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       39.29        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9OY 
       20.91        41.19        19.36        12.20         8.42         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZR TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
        6.15        17.75         5.82        25.78        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-AA1N TCGA-XJ-A83F TCGA-XJ-A83H 
      109.58        85.18        60.92        44.88        37.05        42.08 
TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       48.03        37.25        41.49        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8HM 
       47.15        32.19        25.48         4.87        49.02        48.72 
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        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79        14.04        53.36        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       49.91        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU 
       29.85        20.28        19.17        12.43        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.16        22.75        13.48         4.34 

$`DEL PEAK 26(13Q14.13) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       25.35        20.22         6.97        13.97         1.97        24.03 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5766 
       13.02        35.01         1.02         0.92        12.00         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5494 
       15.06         2.04         9.99        32.02        33.01        27.16 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       13.32        29.79        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 
       27.19        38.93        60.23        47.80        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7125 
       43.07        38.76        60.23        47.87        29.06        93.70 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 
       36.13        37.81        35.18        30.35        27.68        24.39 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 
       20.55        14.14        19.59        17.29         3.75        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       77.16        38.10        21.60        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
       23.80        21.96        23.34        12.92        13.71        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       14.83        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
       10.82         9.27         9.83         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       28.41        13.45        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        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       68.68        46.16        50.70        49.35        47.15        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       45.30        39.39         3.32        40.18        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 
       26.66        31.50        25.15        27.29        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       50.73        35.34        28.18        32.68        26.01        23.93 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7211 
       30.94         3.68        19.76         2.93        37.35         0.79 
TCGA-HC-7230 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 
        1.68        44.55         0.72        23.57         1.48        23.70 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
       26.04         1.97        25.71        30.51        30.84        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AQ 
       22.55        22.32        15.88         1.78         2.20         3.48 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67N TCGA-J4-A67O 
       18.84        88.24        82.92        12.30        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       32.05        29.92         6.02        25.28        27.91        16.83 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J9-A52C 
       10.78        23.67        20.28        11.77        13.55         5.85 
TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       13.32        40.67        30.71        59.67        19.96        44.35 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A6E3 
        8.65        19.66         8.88        11.57       113.10        67.59 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       52.93        58.36        27.02        51.68        49.94        32.84 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        29.56        67.99       101.79        65.82        31.79 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       67.43        69.27        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC 
        5.19        21.14        12.62        25.08        29.23         5.69 
TCGA-QU-A6IN TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
      140.19        86.14        18.12        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A9OF 
       14.73        53.16        52.08        30.38        15.58        38.93 
TCGA-V1-A9OT TCGA-V1-A9Z7 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K 
       15.65         4.27        49.87         4.70         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      111.39        97.41        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 
       53.36        42.94        14.76        45.47        32.19         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        31.99        31.96        40.04 
TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8SH TCGA-YL-A8SP TCGA-YL-A8SR 
       51.81        52.96        51.45        28.77        71.34         8.98 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A9KY TCGA-ZG-A9L6 TCGA-ZG-A9LN 
       28.34         3.09        14.53         4.27        22.59         3.78 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       17.98        14.96        11.47 

  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                           0.76                            0.72 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                         165.17                          140.19 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                         28.965                          25.350 
[1] "0.8 - 165.2 (29.0)" "0.7 - 140.2 (25.4)"
[1] "hr=" "1.4"
D54V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 26(13Q14.13) MUTATED    70 145   6
  DEL PEAK 26(13Q14.13) WILD-TYPE 118 136   4
D54V3, multiclass
    clus
vv   DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  T2                            70                             118
  T3                           145                             136
  T4                             6                               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"
D54V4, binary
                                 cls
clus                                0   1
  DEL PEAK 26(13Q14.13) MUTATED   156  41
  DEL PEAK 26(13Q14.13) WILD-TYPE 182  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q14.13) MUTATED    156   41
  DEL PEAK 26(13Q14.13) WILD-TYPE  182   34
   clus
vv  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  0                           156                             182
  1                            41                              34
[1] 2 2
[1] FALSE
D54V5, binary
                                 cls
clus                                0   1
  DEL PEAK 26(13Q14.13) MUTATED     4 217
  DEL PEAK 26(13Q14.13) WILD-TYPE  10 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q14.13) MUTATED      4  217
  DEL PEAK 26(13Q14.13) WILD-TYPE   10  251
                                        clus
vv                                       DEL PEAK 26(13Q14.13) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              217
                                        clus
vv                                       DEL PEAK 26(13Q14.13) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                251
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(13Q14.13) MUTATED   124  79   1   9
  DEL PEAK 26(13Q14.13) WILD-TYPE 186  59   4   6
D54V6, multiclass
    clus
vv   DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  R0                           124                             186
  R1                            79                              59
  R2                             1                               4
  RX                             9                               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"
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   167   1
  DEL PEAK 27(13Q22.1) WILD-TYPE 306   7
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           168                            313 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                             1                              7 
$`DEL PEAK 27(13Q22.1) MUTATED`
TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5752 
       11.51         2.99         1.02        12.99        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 
        2.04        44.02        23.01        24.03        13.02        26.99 
TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 
       29.00        33.11        19.56        23.90        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 
       48.53        36.23        46.55        52.27        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       36.66        74.10        83.57        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.09         6.28        23.90        38.37        25.87        25.68 
TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7794 TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-8474 
       14.53        18.15        23.05        76.41        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A65J TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-EJ-A8FO 
       20.58        14.83         8.22        15.58         4.21         9.27 
TCGA-EJ-A8FS TCGA-FC-7961 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6348 
        8.75        15.42        41.62        81.04        66.67        49.81 
TCGA-G9-6365 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-7510 TCGA-G9-7519 
       44.81        37.97        25.15        58.22        38.96        27.91 
TCGA-G9-7521 TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 
       30.97        65.26        36.36        28.60        40.08         2.37 
TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7747 TCGA-HC-7819 TCGA-HC-7821 
       38.17         2.10        31.69        24.59        17.85        31.43 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AP 
        1.15        22.36         0.76         2.01         1.61         2.33 
TCGA-HC-A6AS TCGA-HI-7168 TCGA-J4-8198 TCGA-J4-A67M TCGA-J4-A67S TCGA-J4-A83J 
        1.45        78.61        20.19        30.94        27.39        22.88 
TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KK-A59X TCGA-KK-A59Z 
       13.87        10.62        15.22        12.69        56.28        86.40 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
      115.86        54.54       115.13       113.33        67.07        58.19 
TCGA-KK-A7B0 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I9 
       32.84        29.56        20.94       101.79        21.96        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IM 
       63.48         2.73        26.43        82.36        66.18        47.28 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-V1-A8WV 
       13.15        34.85        29.23        41.00        13.32        22.55 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-V1-A9OQ 
       58.39        79.73         6.71        20.91        19.36        12.20 
TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88L TCGA-VP-A875 
        8.42         4.27         4.70         5.82        24.53        75.91 
TCGA-VP-A876 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-AA1N TCGA-XJ-A83F TCGA-XJ-A9DI 
      109.58        85.18        60.92        44.88        37.05        48.03 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJT TCGA-XK-AAK1 
       37.25        40.04        41.49        41.39        47.15        32.19 
TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC 
        4.87        49.02        48.72        60.56        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A9KY 
       62.79        14.04        53.36        62.37        28.34         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       11.67        37.94        36.43        29.85        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.43        16.96        19.04        22.75        11.47         4.34 

$`DEL PEAK 27(13Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 
       25.35        31.96        30.31        20.22         6.97        22.06 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5753 
       13.97         1.97        24.03         1.02        13.02         1.02 
TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 
        0.92        12.00         1.02         1.02        15.06         2.04 
TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-EJ-5494 
       15.98         9.99        32.02        33.01         2.99        27.16 
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-5512 TCGA-EJ-5515 
       28.93        30.31        27.19        38.93        38.53        60.23 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       47.80        64.50        68.35        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7312 
       41.85        47.87        29.06        88.34        93.70        36.13 
TCGA-EJ-7314 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7785 
       37.81        35.18        30.35        27.68        24.39        20.55 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 
       14.14        19.59        17.29         3.75        19.92        77.16 
TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       38.10        21.60        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
        7.56        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A8FN TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
       10.82         9.83         4.54         4.31         4.77        28.41 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       13.45        22.36        17.23        16.24         1.78        87.35 
TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 
       67.99        83.87        55.76        18.21        68.68        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-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       39.39         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 
       26.66        31.50        58.45        27.29        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       50.73        52.93        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-7079 
       23.93         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7233 
       37.35        14.47        28.54         0.79         1.68        44.55 
TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 
        0.72        23.57         1.48         1.68        23.70        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
        1.97        17.16        25.71        30.51        30.84        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A631 
       22.55        17.95        22.32         1.58        15.88         1.78 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.20        17.42         3.48         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        4.93         9.53        25.48        18.84        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O 
       43.69        12.30        33.01        25.32        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       32.05        29.92         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV 
       22.52        10.78        23.67        14.37        20.28        11.77 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KC-A4BL 
       13.55        27.12         5.85        13.32        40.67        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E0 
       19.66         8.88        11.57       113.10        44.68        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      165.17        67.59        49.25         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        34.65        51.68        49.94        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8II 
       67.99        65.82        31.79        67.43        69.27       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        51.39        20.65         5.19        21.14        12.62 
TCGA-M7-A723 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12        11.90        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OT TCGA-V1-A9OY 
       15.58         6.64        38.93        41.19        15.65         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M 
        6.15        17.75        49.87         8.84        25.51         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      111.39        97.41        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 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        42.08         9.04         2.99        31.99        31.96 
TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL 
       30.58        36.95        51.81        25.48        52.96        51.45 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SP TCGA-YL-A8SR 
       71.77        62.14        16.83        28.77        71.34         8.98 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       60.99        24.33        49.91         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       10.13        22.59         3.78        12.16        17.98        14.96 
TCGA-ZG-A9ND 
       13.48 

  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                          0.76                           0.72 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                        115.86                         165.17 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                        30.395                         25.350 
[1] "0.8 - 115.9 (30.4)" "0.7 - 165.2 (25.4)"
[1] "hr=" "4.7"
D55V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 27(13Q22.1) MUTATED    50 111   8
  DEL PEAK 27(13Q22.1) WILD-TYPE 138 170   2
D55V3, multiclass
    clus
vv   DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  T2                           50                            138
  T3                          111                            170
  T4                            8                              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"
D55V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q22.1) MUTATED   121  34
  DEL PEAK 27(13Q22.1) WILD-TYPE 217  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q22.1) MUTATED    121   34
  DEL PEAK 27(13Q22.1) WILD-TYPE  217   41
   clus
vv  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  0                          121                            217
  1                           34                             41
[1] 2 2
[1] FALSE
D55V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q22.1) MUTATED     3 166
  DEL PEAK 27(13Q22.1) WILD-TYPE  11 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q22.1) MUTATED      3  166
  DEL PEAK 27(13Q22.1) WILD-TYPE   11  302
                                        clus
vv                                       DEL PEAK 27(13Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             166
                                        clus
vv                                       DEL PEAK 27(13Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               302
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(13Q22.1) MUTATED    94  61   1   7
  DEL PEAK 27(13Q22.1) WILD-TYPE 216  77   4   8
D55V6, multiclass
    clus
vv   DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  R0                           94                            216
  R1                           61                             77
  R2                            1                              4
  RX                            7                              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"
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    64   2
  DEL PEAK 28(15Q21.3) WILD-TYPE 409   6
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            66                            415 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                             2                              6 
$`DEL PEAK 28(15Q21.3) MUTATED`
TCGA-2A-A8VO TCGA-4L-AA1F TCGA-CH-5740 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       43.79        11.51         1.02        35.01        31.00         1.02 
TCGA-CH-5761 TCGA-EJ-5507 TCGA-EJ-5524 TCGA-EJ-7783 TCGA-FC-A4JI TCGA-G9-6369 
        0.92        23.90        43.07        25.87        13.45        39.95 
TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7749 
       30.97        23.93        37.35        40.08         2.37         1.97 
TCGA-HC-7752 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8264 TCGA-HC-8266 
       25.71        31.43        22.42        28.27         1.58         1.15 
TCGA-HC-A631 TCGA-HC-A6AO TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67N TCGA-J9-A52E 
        1.78        17.42        78.61        43.69        16.54        10.62 
TCGA-J9-A8CL TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E6 
       13.32        19.66        56.28        86.40        30.02       113.33 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A8IA TCGA-KK-A8II TCGA-V1-A8WS TCGA-V1-A8WV 
        6.44        29.56        63.48       113.98        15.58        22.55 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 
       58.39        79.73        19.36        44.91       111.39        75.91 
TCGA-XJ-A83F TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HO 
       37.05        37.25        41.49        30.58        47.15        71.77 
TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A9KY TCGA-ZG-A9L0 
       56.52        62.79        14.04        24.33         4.27        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       29.85        20.28        12.43        22.75        17.98        11.47 

$`DEL PEAK 28(15Q21.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        32.71        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
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-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-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-5508 
       26.30        45.73        28.93        30.31        27.19        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-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        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-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        4.31         4.77        28.41        15.42        22.36        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        83.87        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-G9-6370 
       45.30        39.39        44.81         3.32        40.18        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        58.45        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        64.18        50.73        52.93 
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-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       36.36        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 
        1.48         1.68        23.70        24.59        26.04        17.16 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8257 
       30.51        30.84        17.85        24.56        19.36        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 
        2.17         2.27        22.55        17.95        22.32        15.88 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP 
       22.36         0.76         2.01         2.20         1.61         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        9.53        25.48        18.84        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        33.01        25.32        30.94        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM 
       11.77        13.55        27.12        13.87         5.85        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         8.65         8.88        11.57       113.10 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       44.68       115.86        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       49.25        67.07        58.19        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       18.84         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       86.14        18.12        11.90        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       30.38         6.64         6.71        20.91        38.93        41.19 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65         8.42         5.59         4.27         6.15 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       17.75        49.87         4.70         5.82         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R 
       24.53         6.21        15.52        15.81        41.42        25.78 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       16.31       109.58        97.41        23.93        85.18        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        53.36        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        45.47        32.19         3.91        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       41.39        36.95        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        41.46        45.14        28.77        53.06        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI 
       46.29        32.45       114.38        71.34         8.98        53.36 
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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LB 
       13.28        10.13        37.94        36.43        22.59        19.17 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND 
        3.78        16.96        19.04        12.16        14.96        13.48 
TCGA-ZG-A9NI 
        4.34 

  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                          0.92                           0.72 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                        113.98                         165.17 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                         27.07                          26.66 
[1] "0.9 - 114.0 (27.1)" "0.7 - 165.2 (26.7)"
[1] "hr=" "2.3"
D56V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 28(15Q21.3) MUTATED     9  53   4
  DEL PEAK 28(15Q21.3) WILD-TYPE 179 228   6
D56V3, multiclass
    clus
vv   DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  T2                            9                            179
  T3                           53                            228
  T4                            4                              6
[1] 3 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    38  20
  DEL PEAK 28(15Q21.3) WILD-TYPE 300  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q21.3) MUTATED     38   20
  DEL PEAK 28(15Q21.3) WILD-TYPE  300   55
   clus
vv  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  0                           38                            300
  1                           20                             55
[1] 2 2
[1] FALSE
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q21.3) MUTATED     3  63
  DEL PEAK 28(15Q21.3) WILD-TYPE  11 405
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q21.3) MUTATED      3   63
  DEL PEAK 28(15Q21.3) WILD-TYPE   11  405
                                        clus
vv                                       DEL PEAK 28(15Q21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              63
                                        clus
vv                                       DEL PEAK 28(15Q21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               405
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(15Q21.3) MUTATED    36  26   1   2
  DEL PEAK 28(15Q21.3) WILD-TYPE 274 112   4  13
D56V6, multiclass
    clus
vv   DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  R0                           36                            274
  R1                           26                            112
  R2                            1                              4
  RX                            2                             13
[1] 4 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   182   3
  DEL PEAK 29(16Q22.3) WILD-TYPE 291   5
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           185                            296 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                             3                              5 
$`DEL PEAK 29(16Q22.3) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5753 
       32.71        25.35        22.06         1.97        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5764 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5496 
        2.04         1.02        26.99        33.01        33.11        19.56 
TCGA-EJ-5498 TCGA-EJ-5508 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5521 
       29.79        38.93        48.53        36.23        46.55        51.88 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7318 TCGA-EJ-7321 
       36.66        39.75        74.10        36.13        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       30.35        27.68        23.90        25.87        25.68        20.55 
TCGA-EJ-7789 TCGA-EJ-7794 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46F 
       18.15        23.05        76.41        38.10        24.85        25.74 
TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-FC-7961 
       12.92        18.41         8.22        15.58         4.21        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6343 
       13.45        22.36        16.24        41.62        55.76        18.21 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6373 TCGA-G9-6379 TCGA-G9-6384 
       49.35        46.52        47.44        26.66        58.45        25.15 
TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-A6BY 
       56.75        50.73        30.97        28.18        23.93         3.68 
TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7233 
       14.47         0.79        28.60        40.08        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8216 
        0.72         1.48         1.97        17.85        31.43        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-A6AO TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8CY TCGA-HC-A8D0 
       17.42         1.25         4.41         7.00         9.53        25.48 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83N 
       78.61        43.69        16.54        22.52        22.88        20.28 
TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BV 
       13.55        13.87        13.32        15.22        12.69        43.66 
TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
       21.86        19.66       113.10        56.28        86.40       115.86 
TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP 
      165.17       115.13        49.25       113.33        67.07         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       58.36        27.02        51.68        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IG 
       21.96        65.82        31.79        63.48        26.43        82.36 
TCGA-KK-A8IK TCGA-KK-A8IM TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO 
       51.39        47.28        29.23         5.69         3.19       122.17 
TCGA-SU-A7E7 TCGA-V1-A8MG TCGA-V1-A8MU TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       18.12        28.18        53.16        15.58        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-V1-A9ZG TCGA-V1-A9ZI 
       58.39        79.73        20.91        19.36        49.87         4.70 
TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88Q TCGA-VP-A875 
        5.82        25.51         6.21        15.52        44.91        75.91 
TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
      109.58        23.93        60.92        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJP 
       45.47        38.04        42.08        31.99        31.96        41.39 
TCGA-XK-AAJR TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       36.95        49.02        51.45        48.72        71.77        60.56 
TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       41.46        45.86        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9KY TCGA-ZG-A9L0 
        8.98        62.37        24.33        49.91         4.27        11.67 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU 
       36.43        29.85        20.28        19.17        12.43        19.04 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       22.75        17.98        14.96        11.47        13.48 

$`DEL PEAK 29(16Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF 
       20.42        43.79        22.06        33.96         3.68        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 
       30.31        20.22        11.51         2.99         6.97         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       12.99        13.97        24.03         1.02        13.02        31.00 
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-5789 TCGA-CH-5790 
       24.03         2.04        13.02        15.98         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 
        2.99        29.00        27.16        13.32        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-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 
       48.13        36.69        38.53        60.23        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       64.50        68.35        43.07        38.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       47.87        29.06        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7325 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       33.14        25.35        35.18         6.28        24.39        38.37 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 
       14.53        14.14        19.59        17.29         3.75        19.92 
TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G 
       77.16        25.18        21.60        20.58        17.23        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       23.80        21.96        23.34        13.71        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
        7.56        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
        4.77        28.41        17.23         1.78        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       67.99        66.67        83.87        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       50.70        47.15        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-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       27.29        58.22        64.18        52.93        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 
       35.34        32.68        26.01         6.08        30.94        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7230 
       65.26         2.93        36.36        37.35        28.54         1.68 
TCGA-HC-7231 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 
        2.37         2.10        31.69        23.57         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        26.04        17.16        25.71        30.51        30.84 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       24.56        19.36        28.27         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A6AL TCGA-HC-A6AN 
       17.95        22.32         1.58        15.88         2.20         1.61 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A76X TCGA-HC-A8D1 TCGA-HI-7169 
        2.33         3.48         1.45         4.93        18.84        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        33.01        25.32        30.94 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       27.91        16.83        10.78        23.67        14.37        11.77 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN 
       27.12         5.85        10.62        40.67        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59Y 
       19.96        44.35         8.65         8.88        11.57        44.68 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AW 
       30.02        54.54        67.59        58.19        52.93        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I9 
       49.94        32.84        34.95        36.13        29.56        32.91 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
        2.73        67.43        69.27        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT 
       25.08        18.84        41.00       140.19        86.14        11.90 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       13.32        41.23        40.44        16.70        14.73        39.29 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ 
       52.08        30.38         6.71        38.93        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 
        8.84        24.53        15.81        41.42        25.78        16.31 
TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      111.39        97.41        85.18        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A9DI TCGA-XJ-A9DK 
       53.36        32.19         3.91        37.05        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT 
        2.99        37.25        40.04        41.49        30.58        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8S8 
       51.81        32.19        25.48         4.87        52.96        62.14 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       16.83        56.52        45.14        28.77        53.06        46.29 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        28.34         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS 
       13.28        10.13        37.94        22.59         3.78        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9NI 
       12.16         4.34 

  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                          0.72                           0.92 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                        165.17                         140.19 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                        27.020                         26.025 
[1] "0.7 - 165.2 (27.0)" "0.9 - 140.2 (26.0)"
[1] "hr=" "1.8"
D57V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 29(16Q22.3) MUTATED    53 126   6
  DEL PEAK 29(16Q22.3) WILD-TYPE 135 155   4
D57V3, multiclass
    clus
vv   DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  T2                           53                            135
  T3                          126                            155
  T4                            6                              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   128  39
  DEL PEAK 29(16Q22.3) WILD-TYPE 210  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q22.3) MUTATED    128   39
  DEL PEAK 29(16Q22.3) WILD-TYPE  210   36
   clus
vv  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  0                          128                            210
  1                           39                             36
[1] 2 2
[1] FALSE
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q22.3) MUTATED     5 180
  DEL PEAK 29(16Q22.3) WILD-TYPE   9 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q22.3) MUTATED      5  180
  DEL PEAK 29(16Q22.3) WILD-TYPE    9  288
                                        clus
vv                                       DEL PEAK 29(16Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             180
                                        clus
vv                                       DEL PEAK 29(16Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               288
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(16Q22.3) MUTATED   108  65   1   5
  DEL PEAK 29(16Q22.3) WILD-TYPE 202  73   4  10
D57V6, multiclass
    clus
vv   DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  R0                          108                            202
  R1                           65                             73
  R2                            1                              4
  RX                            5                             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"
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   204   2
  DEL PEAK 30(16Q24.1) WILD-TYPE 269   6
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           206                            275 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                             2                              6 
$`DEL PEAK 30(16Q24.1) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 
       32.71        25.35        11.51        22.06         1.97        35.01 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5766 
        1.02         2.04         0.92        44.02         1.02         1.02 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-EJ-5495 
       13.02        26.99        32.02        33.01         2.99        33.11 
TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5508 TCGA-EJ-5510 
       19.56        29.79        46.52        44.88        38.93        36.69 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       48.53        36.23        46.55        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 
       39.75        74.10        36.13        37.81        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 
       35.18        30.35        27.68        23.90        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46F 
       20.55        18.15        76.41        38.10        24.85        25.74 
TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-EJ-AB27 
       12.92        18.41         8.22        15.58         4.21         4.77 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A6HD TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6343 
       15.42        13.45        16.24        41.62        55.76        18.21 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 
       49.35        46.52        47.44        26.66        31.50        25.15 
TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-A6BY 
       56.75        50.73        30.97        28.18        23.93         3.68 
TCGA-HC-7078 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7232 
       65.26        14.47         0.79        28.60        40.08        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7819 
       44.55         0.72         1.48        26.04         1.97        17.85 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       31.43        22.42        15.88         1.15        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.01         1.61        17.42         1.25         4.41         7.00 
TCGA-HC-A8D0 TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83J 
       25.48        78.61        43.69        16.54        22.52        22.88 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BV 
       20.28        13.87        13.32        15.22        12.69        43.66 
TCGA-KC-A7FA TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E2 
       19.66       113.10        56.28        86.40       115.86       165.17 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
       49.25       113.33        67.07         6.44        58.36        27.02 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 
       51.68        49.94        20.94        67.99        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK TCGA-KK-A8IM 
       31.79        63.48        26.43        82.36        51.39        47.28 
TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO TCGA-SU-A7E7 TCGA-V1-A8MG 
       29.23         5.69         3.19       122.17        18.12        28.18 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       53.16        52.08        15.58        22.55         6.64        58.39 
TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 TCGA-V1-A9ZG 
       79.73        20.91        41.19        19.36         4.27        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P 
        4.70         5.82        25.51         6.21        15.52        41.42 
TCGA-VN-A88Q TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87J 
       44.91        75.91       109.58        23.93        60.92        53.36 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A83H 
       42.94        44.88        14.76        45.47        38.04        42.08 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HJ TCGA-YL-A8HK 
       31.99        31.96        41.39        36.95        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       51.45        48.72        71.77        60.56        16.83        41.46 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9L0 
       62.37        24.33        49.91        28.34         4.27        11.67 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        36.43        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

$`DEL PEAK 30(16Q24.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF 
       20.42        43.79        22.06        33.96         3.68        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       30.31        20.22         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-5763 
       13.97        24.03         1.02        13.02        31.00        12.00 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 
       23.01        15.06        24.03         2.04        15.98         9.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.00        27.16        13.32        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5512 TCGA-EJ-5515 
       30.31        27.19        23.90        48.13        38.53        60.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5530 
       47.80        52.27        64.50        51.88        68.35        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        47.87        29.06        88.34        93.70        83.57 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 
       33.14        25.35         6.28        24.39        38.37        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-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G 
       77.16        25.18        21.60        20.58        17.23        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       23.80        21.96        23.34        13.71        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
        7.56        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
       28.41        22.36        17.23         1.78        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       67.99        66.67        83.87        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       50.70        47.15        45.30        39.39        44.81         3.32 
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        58.45 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       27.29        58.22        64.18        52.93        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 
       35.34        32.68        26.01         6.08        30.94        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7230 TCGA-HC-7231 
        2.93        36.36        37.35        28.54         1.68         2.37 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10        31.69        23.57         1.68        23.70        24.59 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 
       17.16        25.71        30.51        30.84        24.56        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AP TCGA-HC-A6AQ 
       22.32         1.58         1.78         2.20         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        1.45         4.93         9.53        18.84        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        33.01        25.32        30.94        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       16.83        10.78        23.67        14.37        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN 
       27.12         5.85        10.62        40.67        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       19.96        44.35        21.86         8.65         8.88        11.57 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 
       44.68        30.02        54.54        67.59       115.13        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AW TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       52.93        34.65        32.84        34.95        36.13        29.56 
TCGA-KK-A8I5 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH 
      101.79        32.91         2.73        67.43        69.27        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
      113.98        51.25        20.65         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IN 
       13.15        34.85        25.08        18.84        41.00       140.19 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        11.90        13.32        41.23        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WN TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OQ 
       14.73        39.29        30.38         6.71        38.93        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-VN-A88I 
       15.65         8.42         5.59         6.15        17.75         8.84 
TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 
       24.53        15.81        25.78        16.31       111.39        97.41 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-X4-A8KS TCGA-XA-A8JR 
       85.18        55.56        66.97        21.80        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIV TCGA-XK-AAIW 
       37.05        48.03         9.04         2.99        37.25        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL 
       41.49        30.58        47.15        51.81        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
        4.87        62.14        56.52        45.14        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
       46.29        14.04        53.36        60.99         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS 
       13.28        10.13        22.59         3.78        16.96 

  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                          0.72                           1.02 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                        165.17                         140.19 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                         28.26                          25.32 
[1] "0.7 - 165.2 (28.3)" "1.0 - 140.2 (25.3)"
[1] "hr=" "2.9"
D58V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 30(16Q24.1) MUTATED    56 144   6
  DEL PEAK 30(16Q24.1) WILD-TYPE 132 137   4
D58V3, multiclass
    clus
vv   DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  T2                           56                            132
  T3                          144                            137
  T4                            6                              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   144  42
  DEL PEAK 30(16Q24.1) WILD-TYPE 194  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.1) MUTATED    144   42
  DEL PEAK 30(16Q24.1) WILD-TYPE  194   33
   clus
vv  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  0                          144                            194
  1                           42                             33
[1] 2 2
[1] FALSE
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.1) MUTATED     6 200
  DEL PEAK 30(16Q24.1) WILD-TYPE   8 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.1) MUTATED      6  200
  DEL PEAK 30(16Q24.1) WILD-TYPE    8  268
                                        clus
vv                                       DEL PEAK 30(16Q24.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             200
                                        clus
vv                                       DEL PEAK 30(16Q24.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               268
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(16Q24.1) MUTATED   124  69   2   5
  DEL PEAK 30(16Q24.1) WILD-TYPE 186  69   3  10
D58V6, multiclass
    clus
vv   DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  R0                          124                            186
  R1                           69                             69
  R2                            2                              3
  RX                            5                             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"
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   150   4
  DEL PEAK 31(17P13.1) WILD-TYPE 323   4
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           154                            327 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                             4                              4 
$`DEL PEAK 31(17P13.1) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8VT TCGA-2A-A8W3 TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5754 
       20.42        32.71        25.35        11.51        35.01         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5790 TCGA-CH-5791 
        0.92        44.02         1.02         1.02        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       29.00        23.90        36.23        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-7315 TCGA-EJ-7318 
       43.07        36.66        38.76        39.75        33.14        33.83 
TCGA-EJ-7321 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7797 TCGA-EJ-8474 TCGA-EJ-A46F 
       27.09        27.68        23.90        19.92        25.18        25.74 
TCGA-EJ-A65J TCGA-EJ-A7NH TCGA-FC-A4JI TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6354 
       14.83        15.58        13.45        83.87        55.76        49.35 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 
       26.66        31.50        25.15        58.22        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 
       38.96        30.97        26.01        23.93        65.26        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       40.08         1.68         2.37         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8257 TCGA-HC-8266 TCGA-HC-A48F 
       24.59        31.43        22.42        23.87         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8CY 
        0.76         1.78         2.01         4.41         7.00         9.53 
TCGA-HC-A8D0 TCGA-HI-7168 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A83I TCGA-J9-A52B 
       25.48        78.61        33.01        25.32        22.52        13.87 
TCGA-J9-A52E TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A59Y TCGA-KK-A59Z 
       10.62        43.66         8.65        19.66        44.68        86.40 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AP 
      115.86        54.54       165.17       115.13       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AY TCGA-KK-A7B4 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA 
       58.36        51.68        20.94        21.96        31.79        63.48 
TCGA-KK-A8IC TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-KK-A8IL 
       67.43        82.36        66.18       113.98        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-SU-A7E7 
       47.28        21.14        18.84         5.69       140.19        18.12 
TCGA-V1-A8MF TCGA-V1-A8ML TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O5 
       41.23        14.73        30.38        15.58        22.55        58.39 
TCGA-V1-A9O9 TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-V1-A9ZR 
        6.71        19.36        15.65         4.27         4.70         5.82 
TCGA-VN-A88L TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87C 
       24.53        44.91       111.39        75.91       109.58        55.56 
TCGA-VP-A87D TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XK-AAIV 
       60.92        42.94        44.88        14.76        45.47        37.25 
TCGA-XK-AAJA TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8SA 
       30.58        52.96        49.02        51.45        71.77        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       56.52        41.46        45.14        45.86        46.29        32.45 
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 
TCGA-ZG-A9L0 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       11.67        36.43        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LU TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       19.04        17.98        11.47         4.34 

$`DEL PEAK 31(17P13.1) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO 
       43.79        22.06        33.96         3.68        31.96        30.31 
TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       20.22         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       13.97         1.97        24.03         1.02        13.02        31.00 
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        12.00        23.01        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 
       13.02        15.98        26.99         9.99         2.99        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-5508 
       26.30        45.73        28.93        30.31        27.19        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-5518 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       47.80        52.27        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 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7317 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       25.35        35.18        30.35         6.28        24.39        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-8468 TCGA-EJ-8469 
       19.59        17.29         3.75        23.05        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G 
       38.10        24.85        21.60        20.58        17.23        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        58.45        27.29        56.75        64.18 
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        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       28.54         0.79        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       31.69        23.57        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 
       30.51        30.84        17.85        24.56        19.36        28.27 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        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        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A76X TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.93        18.84        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       43.69        20.19        12.30        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.88        10.78        23.67        14.37        20.28 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CM 
       11.77        13.55        27.12         5.85        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A6E0 
       21.86         8.88        11.57       113.10        56.28        30.02 
TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV 
       67.59        49.25        67.07        58.19        52.93        27.02 
TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       34.65        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID 
       67.99       101.79        65.82        32.91         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IJ TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       26.43        51.25         5.19        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP 
       25.08        29.23         3.19        41.00       122.17        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MM 
       11.90        13.32        28.18        40.44        16.70        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OF 
       53.16        52.08         6.64        79.73        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       41.19        12.20         8.42         5.59         6.15        17.75 
TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
       49.87         8.84        25.51         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       41.42        25.78        16.31        97.41        23.93        85.18 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       66.97        21.80        53.36        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        40.04        41.49        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8S8 
       51.81        32.19        25.48         4.87        48.72        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WI 
       60.56        28.77        53.06       114.38         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        49.91         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY 
        4.27        37.94        22.59         3.78        16.96        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9ND 
       22.75        14.96        13.48 

  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                          0.76                           0.72 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                        165.17                         122.17 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                        29.425                         25.710 
[1] "0.8 - 165.2 (29.4)" "0.7 - 122.2 (25.7)"
[1] "hr=" "1.2"
D59V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 31(17P13.1) MUTATED    39 109   6
  DEL PEAK 31(17P13.1) WILD-TYPE 149 172   4
D59V3, multiclass
    clus
vv   DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  T2                           39                            149
  T3                          109                            172
  T4                            6                              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"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.1) MUTATED   104  36
  DEL PEAK 31(17P13.1) WILD-TYPE 234  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.1) MUTATED    104   36
  DEL PEAK 31(17P13.1) WILD-TYPE  234   39
   clus
vv  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  0                          104                            234
  1                           36                             39
[1] 2 2
[1] FALSE
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.1) MUTATED     5 149
  DEL PEAK 31(17P13.1) WILD-TYPE   9 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.1) MUTATED      5  149
  DEL PEAK 31(17P13.1) WILD-TYPE    9  319
                                        clus
vv                                       DEL PEAK 31(17P13.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             149
                                        clus
vv                                       DEL PEAK 31(17P13.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               319
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(17P13.1) MUTATED    91  56   0   4
  DEL PEAK 31(17P13.1) WILD-TYPE 219  82   5  11
D59V6, multiclass
    clus
vv   DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  R0                           91                            219
  R1                           56                             82
  R2                            0                              5
  RX                            4                             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"
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    89   3
  DEL PEAK 32(17Q21.31) WILD-TYPE 384   5
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             92                             389 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                              3                               5 
$`DEL PEAK 32(17Q21.31) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5740 
       20.42        43.79        32.71        11.51        22.06         1.02 
TCGA-CH-5744 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5768 TCGA-CH-5771 
        1.97        13.02        35.01        31.00        24.03        13.02 
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5516 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5542 
       23.90        48.53        46.55        51.88        43.07        29.06 
TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7325 TCGA-EJ-7781 TCGA-EJ-7788 TCGA-EJ-7793 
       37.81        33.83        35.18        23.90        14.14         3.75 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A7NF TCGA-G9-6339 TCGA-G9-6348 
       24.85        25.18        25.74         8.22        83.87        49.81 
TCGA-G9-6377 TCGA-G9-6499 TCGA-HC-7075 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7213 
       31.50        50.73        19.76        37.35        14.47        40.08 
TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8262 
        1.68        26.04        24.56        19.36        22.42        22.32 
TCGA-HC-A48F TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D1 
       22.36         3.48         1.45         4.93         9.53        18.84 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67S 
       78.61        43.69        20.19        33.01        25.32        27.39 
TCGA-J4-A67T TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BV 
        6.02        14.37        13.87        10.62        15.22        43.66 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IA 
      115.13       113.33         6.44       101.79        21.96        63.48 
TCGA-KK-A8IG TCGA-KK-A8II TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IP TCGA-V1-A9OL 
       82.36       113.98        18.84         5.69        86.14        19.36 
TCGA-V1-A9ZR TCGA-VN-A88M TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87C TCGA-VP-AA1N 
        5.82         6.21       111.39        75.91        55.56        44.88 
TCGA-X4-A8KQ TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SA 
       45.47        30.58        47.15        52.96        71.77        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-ZG-A9L4 TCGA-ZG-A9L9 
       56.52        41.46        46.29        62.79        36.43        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9M4 
       12.43        17.98 

$`DEL PEAK 32(17Q21.31) WILD-TYPE`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       22.06        33.96         3.68        25.35        31.96        30.31 
TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 
       20.22         2.99         6.97        12.99        13.97        24.03 
TCGA-CH-5748 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
        1.02         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5772 
        1.02        23.01         1.02        15.06         2.04        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-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        48.13        36.69        38.53        36.23        60.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 
       47.80        52.27        64.50        68.35        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        41.85        47.87        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 
       93.70        83.57        36.13        33.14        25.35        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        18.15        19.59        17.29 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46B 
       23.05        19.92        77.16        76.41        38.10        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 
       67.99        66.67        55.76        18.21        68.68        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-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.31        26.66        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        52.93        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        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        65.26         2.93        36.36 
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        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       30.84        17.85        31.43        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        2.27        22.55        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        17.42 
TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8D0 TCGA-HI-7169 
        2.33         1.25         4.41         7.00        25.48        88.24 
TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       82.92        12.30        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
       29.92        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        20.28        11.77        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
        5.85        13.32        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       19.96        44.35        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 
       30.02        54.54       165.17        67.59        49.25        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC 
       67.99        65.82        31.79        32.91         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       69.27        26.43        66.18        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        29.23         3.19        41.00       140.19       122.17 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        11.90        13.32        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       15.58        22.55         6.64        58.39        79.73         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       20.91        38.93        41.19        12.20        15.65         8.42 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
        5.59         4.27         6.15        17.75        49.87         4.70 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51        24.53        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78        16.31       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       85.18        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 
       40.04        41.49        41.39        36.95        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48         4.87        49.02        51.45        48.72        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        53.06        45.86        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34         8.98        14.04        53.36        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         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L5 
       13.28        10.13         4.27        11.67        37.94        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       22.59        19.17         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        14.96        11.47        13.48         4.34 

  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                           1.02                            0.72 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                         115.13                          165.17 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                          25.53                           27.02 
[1] "1.0 - 115.1 (25.5)" "0.7 - 165.2 (27.0)"
[1] "hr=" "2.2"
D60V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 32(17Q21.31) MUTATED    29  61   3
  DEL PEAK 32(17Q21.31) WILD-TYPE 159 220   7
D60V3, multiclass
    clus
vv   DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  T2                            29                             159
  T3                            61                             220
  T4                             3                               7
[1] 3 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    67  13
  DEL PEAK 32(17Q21.31) WILD-TYPE 271  62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(17Q21.31) MUTATED     67   13
  DEL PEAK 32(17Q21.31) WILD-TYPE  271   62
   clus
vv  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  0                            67                             271
  1                            13                              62
[1] 2 2
[1] FALSE
D60V5, binary
                                 cls
clus                                0   1
  DEL PEAK 32(17Q21.31) MUTATED     3  90
  DEL PEAK 32(17Q21.31) WILD-TYPE  11 378
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(17Q21.31) MUTATED      3   90
  DEL PEAK 32(17Q21.31) WILD-TYPE   11  378
                                        clus
vv                                       DEL PEAK 32(17Q21.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               90
                                        clus
vv                                       DEL PEAK 32(17Q21.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                378
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(17Q21.31) MUTATED    61  28   1   2
  DEL PEAK 32(17Q21.31) WILD-TYPE 249 110   4  13
D60V6, multiclass
    clus
vv   DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  R0                            61                             249
  R1                            28                             110
  R2                             1                               4
  RX                             2                              13
[1] 4 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   122   3
  DEL PEAK 33(18Q21.31) WILD-TYPE 351   5
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                            125                             356 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                              3                               5 
$`DEL PEAK 33(18Q21.31) MUTATED`
TCGA-2A-A8VT TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5754 
       32.71         3.68        11.51        22.06        35.01         2.04 
TCGA-CH-5761 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5504 TCGA-EJ-5507 
        0.92         2.04        15.98        33.01        28.93        23.90 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 
       48.53        36.23        47.80        52.27        43.07        36.66 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-8472 
       83.57        36.13        33.14        23.90        23.05        24.85 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-6348 
       21.96        23.34         8.22        15.58        41.62        49.81 
TCGA-G9-6351 TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       46.16        49.35        26.66        31.50        37.97        25.15 
TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7211 TCGA-HC-7213 
       30.97        28.18        26.01        65.26         0.79        40.08 
TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7820 TCGA-HC-7821 
        1.68         1.48        26.04         1.97        24.56        31.43 
TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6HY TCGA-HC-A76W 
       22.42        22.36         0.76         1.78         4.41         7.00 
TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7170 TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A83I 
        9.53        78.61        82.92        25.32        16.54        22.52 
TCGA-J4-A83N TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z 
       20.28        13.32        40.67        19.66        56.28        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      115.86        30.02        54.54        49.25       113.33        67.07 
TCGA-KK-A7AW TCGA-KK-A7B4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8IB TCGA-KK-A8IH 
       34.65        20.94        21.96        65.82         2.73        66.18 
TCGA-KK-A8II TCGA-KK-A8IL TCGA-M7-A724 TCGA-M7-A725 TCGA-TP-A8TV TCGA-V1-A8MJ 
      113.98        20.65        29.23        18.84        13.32        40.44 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9OL TCGA-V1-A9ZI 
       53.16        52.08        22.55        79.73        19.36         4.70 
TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A87B 
       25.51        15.52        41.42        16.31       111.39        85.18 
TCGA-VP-A87C TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJ3 
       55.56        14.76        37.05        38.04        37.25        41.49 
TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       30.58        47.15        49.02        48.72        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       114.38        62.79         8.98        14.04 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       62.37        49.91        28.34        29.85        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9N3 
       12.43        16.96        19.04        22.75        11.47 

$`DEL PEAK 33(18Q21.31) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W3 TCGA-2A-AAYF 
       20.42        43.79        22.06        33.96        25.35        31.96 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       30.31        20.22         2.99         6.97         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
       13.97         1.97        24.03         1.02        13.02        31.00 
TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        1.02        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       15.06        24.03        13.02        26.99         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-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-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       27.19        38.93        48.13        36.69        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5527 
       46.55        64.50        51.88        68.35        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        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       93.70        37.81        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        38.37        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-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
       17.29         3.75        19.92        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.80        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
        7.56        11.61        28.70        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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-G9-6353 
       66.67        83.87        55.76        18.21        68.68        50.70 
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-G9-6379 
        3.32        40.18        39.95        38.01        40.31        58.45 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 
       38.96        27.91        35.34        32.68        23.93         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        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       14.47        28.54        28.60         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 
        0.72         2.10        31.69        23.57         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       24.59        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A632 
       17.95        22.32         1.58        15.88         1.15         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7171 
        1.25         4.93        25.48        18.84        88.24        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q 
       20.19        12.30        33.01        30.94        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        14.37        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CP 
       27.12        13.87         5.85        10.62        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E2 
        8.65         8.88        11.57       113.10        44.68       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       67.59       115.13        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       29.56        67.99       101.79        31.79        32.91        63.48 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK 
       67.43        69.27        26.43        82.36        51.25        51.39 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08         5.69         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK 
       86.14        18.12        11.90        41.23        28.18        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 
       14.73        39.29        30.38        15.58         6.64        58.39 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT 
        6.71        20.91        38.93        41.19        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88Q 
        5.82         8.84        24.53         6.21        15.81        44.91 
TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87D 
       25.78        75.91       109.58        97.41        23.93        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        44.88        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       32.19         3.91        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.99        31.96        40.04        41.39        36.95        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S9 
       32.19        25.48         4.87        52.96        51.45        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        53.06        46.29 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-ZG-A8QW 
       32.45        71.34        53.36        60.99        24.33         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       36.43        22.59         3.78        12.16        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                           0.76                            0.72 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                         115.86                          165.17 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                         28.930                          25.825 
[1] "0.8 - 115.9 (28.9)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1.4"
D61V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 33(18Q21.31) MUTATED    32  90   4
  DEL PEAK 33(18Q21.31) WILD-TYPE 156 191   6
D61V3, multiclass
    clus
vv   DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  T2                            32                             156
  T3                            90                             191
  T4                             4                               6
[1] 3 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    85  29
  DEL PEAK 33(18Q21.31) WILD-TYPE 253  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(18Q21.31) MUTATED     85   29
  DEL PEAK 33(18Q21.31) WILD-TYPE  253   46
   clus
vv  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  0                            85                             253
  1                            29                              46
[1] 2 2
[1] FALSE
D61V5, binary
                                 cls
clus                                0   1
  DEL PEAK 33(18Q21.31) MUTATED     3 123
  DEL PEAK 33(18Q21.31) WILD-TYPE  11 345
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(18Q21.31) MUTATED      3  123
  DEL PEAK 33(18Q21.31) WILD-TYPE   11  345
                                        clus
vv                                       DEL PEAK 33(18Q21.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              123
                                        clus
vv                                       DEL PEAK 33(18Q21.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                345
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(18Q21.31) MUTATED    69  53   0   2
  DEL PEAK 33(18Q21.31) WILD-TYPE 241  85   5  13
D61V6, multiclass
    clus
vv   DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  R0                            69                             241
  R1                            53                              85
  R2                             0                               5
  RX                             2                              13
[1] 4 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   128   3
  DEL PEAK 34(18Q23) WILD-TYPE 345   5
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         131                          350 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                           3                            5 
$`DEL PEAK 34(18Q23) MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       32.71        11.51        35.01         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5504 TCGA-EJ-5507 
       44.02        15.98        33.01        33.11        28.93        23.90 
TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 
       48.53        36.23        47.80        52.27        43.07        36.66 
TCGA-EJ-5527 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-8470 
       39.75        83.57        33.14        23.90        23.05        38.10 
TCGA-EJ-8472 TCGA-EJ-A46D TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A7NF 
       24.85        20.58        21.96        23.34        12.92         8.22 
TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6354 
       15.58        41.62        55.76        49.81        46.16        49.35 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6499 TCGA-G9-7521 
       26.66        31.50        37.97        25.15        50.73        30.97 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 
       28.18        26.01        65.26         0.79        40.08         1.68 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7820 TCGA-HC-7821 
        1.48        23.70        26.04         1.97        24.56        31.43 
TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6HY 
       22.42        22.36         0.76         1.78         1.61         4.41 
TCGA-HC-A76W TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67L 
        7.00         9.53        78.61        82.92        43.69        25.32 
TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83N TCGA-J9-A8CL TCGA-KC-A7FA TCGA-KK-A59Z 
       16.54        22.52        20.28        13.32        19.66        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      115.86        30.02        54.54        49.25       113.33        67.07 
TCGA-KK-A7AW TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8IB 
       34.65        20.94        67.99        21.96        65.82         2.73 
TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-M7-A71Z TCGA-M7-A724 TCGA-M7-A725 
       69.27        66.18       113.98        21.14        29.23        18.84 
TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O7 TCGA-V1-A9ZI 
       13.32        40.44        52.08        22.55        79.73         4.70 
TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A87B 
       25.51        15.52        41.42        16.31       111.39        85.18 
TCGA-VP-A87C TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJT 
       55.56        14.76        37.05        37.25        41.49        47.15 
TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SJ TCGA-YL-A8SO 
       49.02        48.72        71.77        16.83        45.86       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WX 
       71.34        62.79         8.98        14.04        62.37        49.91 
TCGA-YL-A9WY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       28.34        11.67        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       16.96        19.04        22.75        17.98        11.47 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
       13.02        31.00        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-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 
       32.02         2.99        29.00        27.16        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-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       27.19        38.93        48.13        36.69        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5530 
       46.55        64.50        51.88        68.35        38.76        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        88.34        74.10        93.70 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       36.13        37.81        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        38.37        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-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8474 
       17.29         3.75        19.92        77.16        76.41        25.18 
TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A65E 
       21.60        17.23        25.74        21.96        23.80        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       14.20         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6343 
       87.35        81.04        67.99        66.67        83.87        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        58.45        27.29        58.22        56.75        64.18 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S7 
       52.93        38.96        27.91        35.34        32.68        23.93 
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        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 
       37.35        14.47        28.54        28.60         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
       44.55         0.72         2.10        31.69        23.57         1.68 
TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       24.59        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A632 
       17.95        22.32         1.58        15.88         1.15         2.01 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 
        4.93        25.48        18.84        88.24        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       33.01        30.94        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K 
        6.02        25.28        27.91        16.83        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        14.37        11.77        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
        5.85        10.62        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E2 
        8.88        11.57       113.10        56.28        44.68       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       67.59       115.13        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       29.56       101.79        31.79        32.91        63.48        67.43 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       26.43        82.36        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-MG-AAMC 
        5.19        12.62        13.15        34.85        25.08         5.69 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       11.90        41.23        28.18        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O9 
       53.16        30.38        15.58         6.64        58.39         6.71 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88Q 
        5.82         8.84        24.53         6.21        15.81        44.91 
TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87D 
       25.78        75.91       109.58        97.41        23.93        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        44.88        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
       36.95        51.81        32.19        25.48         4.87        52.96 
TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       51.45        62.14        60.56        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WI TCGA-YL-A9WJ 
       28.77        53.06        46.29        32.45        53.36        60.99 
TCGA-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       24.33         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9LY TCGA-ZG-A9MC 
       37.94        36.43        22.59         3.78        12.16        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                        0.76                         0.72 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                      115.86                       165.17 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                      28.930                       25.825 
[1] "0.8 - 115.9 (28.9)" "0.7 - 165.2 (25.8)"
[1] "hr=" "1.3"
D62V2, continuous
                              vv
clus                            T2  T3  T4
  DEL PEAK 34(18Q23) MUTATED    34  94   4
  DEL PEAK 34(18Q23) WILD-TYPE 154 187   6
D62V3, multiclass
    clus
vv   DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  T2                         34                          154
  T3                         94                          187
  T4                          4                            6
[1] 3 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    87  32
  DEL PEAK 34(18Q23) WILD-TYPE 251  43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED     87   32
  DEL PEAK 34(18Q23) WILD-TYPE  251   43
   clus
vv  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  0                         87                          251
  1                         32                           43
[1] 2 2
[1] FALSE
D62V5, binary
                              cls
clus                             0   1
  DEL PEAK 34(18Q23) MUTATED     4 128
  DEL PEAK 34(18Q23) WILD-TYPE  10 340
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED      4  128
  DEL PEAK 34(18Q23) WILD-TYPE   10  340
                                        clus
vv                                       DEL PEAK 34(18Q23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           128
                                        clus
vv                                       DEL PEAK 34(18Q23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             340
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 34(18Q23) MUTATED    74  53   0   2
  DEL PEAK 34(18Q23) WILD-TYPE 236  85   5  13
D62V6, multiclass
    clus
vv   DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  R0                         74                          236
  R1                         53                           85
  R2                          0                            5
  RX                          2                           13
[1] 4 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    48   1
  DEL PEAK 35(19Q13.2) WILD-TYPE 425   7
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            49                            432 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                             1                              7 
$`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        30.35        27.68 
TCGA-EJ-7781 TCGA-EJ-8474 TCGA-EJ-A7NH TCGA-G9-6379 TCGA-G9-7525 TCGA-HC-7078 
       23.90        25.18        15.58        58.45        32.68        65.26 
TCGA-HC-7080 TCGA-HC-7752 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A76W 
       36.36        25.71        22.42        22.36         0.76         7.00 
TCGA-HI-7171 TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-KC-A7FA 
       43.69        14.37        13.87        10.62        13.32        19.66 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B4 TCGA-KK-A8IH TCGA-TP-A8TV 
       49.25       113.33        67.07        20.94        66.18        13.32 
TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9OF TCGA-V1-A9OL TCGA-V1-A9ZR TCGA-VN-A88P 
       52.08        22.55        38.93        19.36         5.82        41.42 
TCGA-WW-A8ZI TCGA-XK-AAJA TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8SB TCGA-YL-A8SJ 
       14.76        30.58         4.87        48.72        56.52        45.86 
TCGA-YL-A8SL TCGA-YL-A9WK TCGA-YL-A9WL TCGA-ZG-A9L5 TCGA-ZG-A9LM TCGA-ZG-A9M4 
       32.45        62.37        24.33        29.85        12.43        17.98 
TCGA-ZG-A9NI 
        4.34 

$`DEL PEAK 35(19Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       25.35        31.96        30.31        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06         1.02        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        31.00         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        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-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-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        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-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7330 
       33.14        25.35        33.83        27.09        35.18         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        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-8472 TCGA-EJ-A46B 
       19.92        77.16        76.41        38.10        24.85        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ 
        7.56        11.61        28.70         8.22        14.20         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
       15.65         4.21        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        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        83.87        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-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       37.97        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        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        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       19.76         2.93        37.35        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        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 
       23.70        24.59        26.04         1.97        17.16        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
       30.84        17.85        24.56        31.43        19.36        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.58        15.88         1.15         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        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        4.41         4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        20.28        11.77        13.55        27.12 
TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
        5.85        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       19.96        44.35        43.66        21.86         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       11.57       113.10        56.28        44.68        86.40       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 
       30.02        54.54       165.17        67.59       115.13        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 
       49.94        32.84        34.95        36.13        29.56        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II 
        2.73        67.43        69.27        26.43        82.36       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
        5.69         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       18.12        11.90        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 
       14.73        39.29        53.16        30.38        15.58         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OQ 
       58.39        79.73         6.71        20.91        41.19        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65         8.42         5.59         4.27         6.15        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       49.87         4.70         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.52        15.81        44.91        25.78        16.31       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        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        53.36        42.94        44.88 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        41.49        41.39        36.95        47.15        51.81 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       32.19        25.48        52.96        49.02        51.45        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 
       53.06        46.29       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        53.36        60.99        49.91        28.34         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 
       14.53        13.28        10.13         4.27        11.67        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LN TCGA-ZG-A9LS 
       36.43        22.59        20.28        19.17         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        14.96        11.47        13.48 

  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                          0.76                           0.72 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                        113.33                         165.17 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                        25.180                         27.005 
[1] "0.8 - 113.3 (25.2)" "0.7 - 165.2 (27.0)"
[1] "hr=" "1.9"
D63V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 35(19Q13.2) MUTATED    11  35   3
  DEL PEAK 35(19Q13.2) WILD-TYPE 177 246   7
D63V3, multiclass
    clus
vv   DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  T2                           11                            177
  T3                           35                            246
  T4                            3                              7
[1] 3 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    36  11
  DEL PEAK 35(19Q13.2) WILD-TYPE 302  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19Q13.2) MUTATED     36   11
  DEL PEAK 35(19Q13.2) WILD-TYPE  302   64
   clus
vv  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  0                           36                            302
  1                           11                             64
[1] 2 2
[1] FALSE
D63V5, binary
                                cls
clus                               0   1
  DEL PEAK 35(19Q13.2) MUTATED     1  48
  DEL PEAK 35(19Q13.2) WILD-TYPE  13 420
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19Q13.2) MUTATED      1   48
  DEL PEAK 35(19Q13.2) WILD-TYPE   13  420
                                        clus
vv                                       DEL PEAK 35(19Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              48
                                        clus
vv                                       DEL PEAK 35(19Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               420
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(19Q13.2) MUTATED    27  22   0   0
  DEL PEAK 35(19Q13.2) WILD-TYPE 283 116   5  15
D63V6, multiclass
    clus
vv   DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  R0                           27                            283
  R1                           22                            116
  R2                            0                              5
  RX                            0                             15
[1] 4 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    49   0
  DEL PEAK 36(21Q22.2) WILD-TYPE 424   8
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            49                            432 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                             0                              8 
$`DEL PEAK 36(21Q22.2) MUTATED`
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5751 TCGA-CH-5753 
       32.71        11.51        12.99        24.03        35.01         1.02 
TCGA-CH-5761 TCGA-CH-5765 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5516 TCGA-EJ-5519 
        0.92        23.01        29.79        46.52        46.55        64.50 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7785 TCGA-EJ-A7NH TCGA-G9-6329 TCGA-G9-6342 
       27.09        35.18        20.55        15.58        41.62        55.76 
TCGA-G9-7521 TCGA-G9-A9S7 TCGA-H9-A6BY TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7821 
       30.97        23.93         3.68         1.68        26.04        31.43 
TCGA-HC-8259 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J9-A52B TCGA-KC-A7FA 
        2.27         6.02        25.28        10.78        13.87        19.66 
TCGA-KC-A7FE TCGA-KK-A8IH TCGA-MG-AAMC TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-VN-A88Q 
       11.57        66.18         5.69        79.73         6.71        44.91 
TCGA-VP-A872 TCGA-VP-A87D TCGA-VP-A87K TCGA-X4-A8KQ TCGA-XK-AAIW TCGA-YL-A8SF 
      111.39        60.92        42.94        45.47        40.04        45.14 
TCGA-YL-A8SJ TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       45.86        24.33        28.34         4.27        22.75        17.98 
TCGA-ZG-A9N3 
       11.47 

$`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-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       31.96        30.31        20.22         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
        1.02        13.97         1.97         1.02        13.02        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5767 
        2.04        44.02        12.00         1.02         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-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       19.56        13.32        44.88        26.30        45.73        28.93 
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-5517 TCGA-EJ-5518 
       48.53        38.53        36.23        60.23        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-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       33.83        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        25.68        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        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        13.45        22.36 
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        83.87        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        58.45        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        64.18        50.73        52.93 
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        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       31.69        23.57         1.48        23.70        24.59         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        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        28.27        23.87         2.17        22.55 
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        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        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        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83L TCGA-J4-A83M 
       27.91        16.83        22.52        22.88        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52E 
       20.28        11.77        13.55        27.12         5.85        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       19.96        44.35        43.66        21.86         8.65         8.88 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
      113.10        56.28        44.68        86.40       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        82.36       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        29.23        18.84         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
      122.17        86.14        18.12        11.90        13.32        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 
       52.08        30.38        15.58        22.55         6.64        58.39 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        41.19        19.36        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
        8.42         5.59         4.27         6.15        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        4.70         5.82         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.52        15.81        41.42        25.78        16.31        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E 
      109.58        97.41        23.93        85.18        55.56        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        53.36        44.88        14.76        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        41.49        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       36.95        47.15        51.81        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        56.52        41.46        28.77        53.06 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A8QW 
       14.04        53.36        60.99        62.37        49.91         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       14.53        13.28        10.13        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        19.04        12.16        14.96        13.48         4.34 

  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                          0.92                           0.72 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                        111.39                         165.17 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                        25.280                         27.005 
[1] "0.9 - 111.4 (25.3)" "0.7 - 165.2 (27.0)"
[1] "hr="     "7.7e+07"
D64V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 36(21Q22.2) MUTATED    10  37   3
  DEL PEAK 36(21Q22.2) WILD-TYPE 178 244   7
D64V3, multiclass
    clus
vv   DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  T2                           10                            178
  T3                           37                            244
  T4                            3                              7
[1] 3 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    32  12
  DEL PEAK 36(21Q22.2) WILD-TYPE 306  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.2) MUTATED     32   12
  DEL PEAK 36(21Q22.2) WILD-TYPE  306   63
   clus
vv  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  0                           32                            306
  1                           12                             63
[1] 2 2
[1] FALSE
D64V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q22.2) MUTATED     3  47
  DEL PEAK 36(21Q22.2) WILD-TYPE  11 421
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.2) MUTATED      3   47
  DEL PEAK 36(21Q22.2) WILD-TYPE   11  421
                                        clus
vv                                       DEL PEAK 36(21Q22.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              47
                                        clus
vv                                       DEL PEAK 36(21Q22.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               421
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(21Q22.2) MUTATED    30  17   0   2
  DEL PEAK 36(21Q22.2) WILD-TYPE 280 121   5  13
D64V6, multiclass
    clus
vv   DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  R0                           30                            280
  R1                           17                            121
  R2                            0                              5
  RX                            2                             13
[1] 4 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   143   2
  DEL PEAK 37(21Q22.3) WILD-TYPE 330   6
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           145                            336 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                             2                              6 
$`DEL PEAK 37(21Q22.3) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5740 
       20.42        32.71        22.06        20.22        11.51         1.02 
TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       12.99        24.03        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5790 
        0.92         1.02        23.01        24.03         2.04        32.02 
TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 
       33.01        29.00        33.11        19.56        13.32        46.52 
TCGA-EJ-5508 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       38.93        38.53        46.55        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5542 TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 
       43.07        38.76        29.06        33.14        33.83        27.09 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-A46F TCGA-EJ-A65F 
       25.87        25.68        76.41        24.85        25.74        18.41 
TCGA-EJ-A7NH TCGA-EJ-A8FS TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6342 
       15.58         8.75        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        52.93        30.97        32.68        23.93 
TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
        3.68        37.35        14.47        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 
       38.17        23.70        26.04        17.85        31.43        19.36 
TCGA-HC-8257 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A76X TCGA-HC-A8D0 
       23.87         2.27        22.32        22.36         4.93        25.48 
TCGA-HC-A8D1 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67S TCGA-J4-A6M7 
       18.84        20.19        33.01        25.32        27.39        16.83 
TCGA-J4-A83K TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7FA 
       10.78        13.87        10.62        15.22        43.66        19.66 
TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 
       11.57        44.68       115.86        54.54       115.13       113.33 
TCGA-KK-A7AU TCGA-KK-A7B1 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I8 
       58.36        34.95        20.94        67.99       101.79        31.79 
TCGA-KK-A8IC TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 
       67.43        66.18       113.98        47.28        21.14        18.84 
TCGA-MG-AAMC TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-V1-A8WS TCGA-V1-A9O7 
        5.69       140.19        86.14        11.90        15.58        79.73 
TCGA-V1-A9O9 TCGA-V1-A9ZG TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q 
        6.71        49.87        25.51        24.53         6.21        44.91 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87K 
      111.39        75.91       109.58        55.56        60.92        42.94 
TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-XK-AAIW TCGA-YL-A8HK TCGA-YL-A8SF TCGA-YL-A8SJ 
       45.47        37.25        40.04        49.02        45.14        45.86 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       32.45        71.34        24.33        28.34        10.13         4.27 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       37.94        36.43        20.28        19.04        22.75        17.98 
TCGA-ZG-A9N3 
       11.47 

$`DEL PEAK 37(21Q22.3) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       43.79        33.96         3.68        25.35        31.96        30.31 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5748 
        2.99         6.97        22.06        13.97         1.97         1.02 
TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5771 
       13.02        44.02        12.00         1.02        15.06        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5498 
       15.98        26.99         9.99         2.99        27.16        29.79 
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-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5515 
       23.90        48.13        36.69        48.53        36.23        60.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       47.80        52.27        36.66        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        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       37.81        25.35        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       24.39        23.90        38.37        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 
       77.16        38.10        25.18        21.60        20.58        17.23 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FO 
       14.20         6.48        15.65         4.21        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7961 TCGA-FC-A4JI 
        9.83         4.54         4.31         4.77        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
       22.36        17.23        16.24         1.78        87.35        81.04 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       66.67        83.87        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       50.70        47.15        46.52         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       38.01        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       56.75        64.18        50.73        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7078 
       28.18        26.01         6.08        30.94        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7233 
        2.93        36.36        28.54         0.79        28.60        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7820 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       24.56        22.42        28.27         2.17        22.55        17.95 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15         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        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7169 
        1.25         4.41         7.00         9.53        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       82.92        43.69        12.30        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83I 
       32.05        29.92         6.02        25.28        27.91        22.52 
TCGA-J4-A83J TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        23.67        14.37        20.28        11.77        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       27.12         5.85        13.32        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD 
       59.67        19.96        44.35        21.86         8.65         8.88 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
      113.10        56.28        86.40        30.02       165.17        67.59 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AV 
       49.25        67.07        58.19         6.44        52.93        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B2 TCGA-KK-A7B3 
       34.65        51.68        49.94        32.84        36.13        29.56 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID 
       21.96        65.82        32.91        63.48         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       26.43        82.36        51.25        51.39        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
       12.62        13.15        34.85        25.08        29.23         3.19 
TCGA-QU-A6IM TCGA-QU-A6IO TCGA-SU-A7E7 TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       41.00       122.17        18.12        13.32        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OF 
       30.38        22.55         6.64        58.39        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       41.19        19.36        12.20        15.65         8.42         5.59 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VN-A88I 
        4.27         6.15        17.75         4.70         5.82         8.84 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 
       15.52        15.81        41.42        25.78        16.31        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N 
       23.93        85.18        66.97        21.80        53.36        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJ3 
       48.03         9.04         2.99        31.99        31.96        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XK-AAK1 
       30.58        41.39        36.95        47.15        51.81        32.19 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48         4.87        52.96        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH 
       62.14        60.56        16.83        56.52        41.46        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       53.06        46.29       114.38        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX 
       53.36        60.99        62.37        49.91         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       13.28        11.67        29.85        22.59        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LY TCGA-ZG-A9MC TCGA-ZG-A9ND TCGA-ZG-A9NI 
        3.78        16.96        12.16        14.96        13.48         4.34 

  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                          0.92                           0.72 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                        140.19                         165.17 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                        29.060                         25.415 
[1] "0.9 - 140.2 (29.1)" "0.7 - 165.2 (25.4)"
[1] "hr=" "2.1"
D65V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 37(21Q22.3) MUTATED    46  93   5
  DEL PEAK 37(21Q22.3) WILD-TYPE 142 188   5
D65V3, multiclass
    clus
vv   DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  T2                           46                            142
  T3                           93                            188
  T4                            5                              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"
D65V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(21Q22.3) MUTATED    98  29
  DEL PEAK 37(21Q22.3) WILD-TYPE 240  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED     98   29
  DEL PEAK 37(21Q22.3) WILD-TYPE  240   46
   clus
vv  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  0                           98                            240
  1                           29                             46
[1] 2 2
[1] FALSE
D65V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(21Q22.3) MUTATED     5 140
  DEL PEAK 37(21Q22.3) WILD-TYPE   9 328
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED      5  140
  DEL PEAK 37(21Q22.3) WILD-TYPE    9  328
                                        clus
vv                                       DEL PEAK 37(21Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             140
                                        clus
vv                                       DEL PEAK 37(21Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               328
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(21Q22.3) MUTATED    93  42   2   6
  DEL PEAK 37(21Q22.3) WILD-TYPE 217  96   3   9
D65V6, multiclass
    clus
vv   DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  R0                           93                            217
  R1                           42                             96
  R2                            2                              3
  RX                            6                              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"
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"
