[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSARC-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/SARC-TP/10006228/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/10013795/transformed.cor.cli.txt"

nPatients in clinical file=114, in cluster file=169, common to both=114
[1]  61 114
[1] "AMP PEAK  1(1P32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           36                            78 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           36                            78 
[1] "AMP PEAK  2(1Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                           45                            69 
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                           45                            69 
[1] "AMP PEAK  3(3P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                           25                            89 
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                           25                            89 
[1] "AMP PEAK  4(5P15.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                           47                            67 
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                           47                            67 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           26                            88 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           26                            88 
[1] "AMP PEAK  6(6Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           32                            82 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           32                            82 
[1] "AMP PEAK  7(7Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                           31                            83 
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                           31                            83 
[1] "AMP PEAK  8(8Q21.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                            42                             72 
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                            42                             72 
[1] "AMP PEAK  9(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                            17                             97 
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                            17                             97 
[1] "AMP PEAK 10(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                             21                              93 
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                             21                              93 
[1] "AMP PEAK 11(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            25                             89 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            25                             89 
[1] "AMP PEAK 12(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          46                           68 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          46                           68 
[1] "AMP PEAK 13(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                          19                           95 
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                          19                           95 
[1] "AMP PEAK 14(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                            38                             76 
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                            38                             76 
[1] "AMP PEAK 15(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                            29                             85 
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                            29                             85 
[1] "AMP PEAK 16(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                            39                             75 
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                            39                             75 
[1] "AMP PEAK 17(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          37                           77 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          37                           77 
[1] "AMP PEAK 18(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                             42                              72 
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                             42                              72 
[1] "AMP PEAK 19(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                            33                             81 
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                            33                             81 
[1] "AMP PEAK 20(XP21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                           36                            78 
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                           36                            78 
[1] "AMP PEAK 21(XQ21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                           18                            96 
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                           18                            96 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            36                             78 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            36                             78 
[1] "DEL PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           18                            96 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           18                            96 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         31                          83 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         31                          83 
[1] "DEL PEAK  4(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                           38                            76 
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                           38                            76 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           41                            73 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           41                            73 
[1] "DEL PEAK  6(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                           43                            71 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                           43                            71 
[1] "DEL PEAK  7(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                            21                             93 
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                            21                             93 
[1] "DEL PEAK  8(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         26                          88 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         26                          88 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           38                            76 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           38                            76 
[1] "DEL PEAK 10(6P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                           40                            74 
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                           40                            74 
[1] "DEL PEAK 11(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                           26                            88 
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                           26                            88 
[1] "DEL PEAK 12(6Q16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                           23                            91 
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                           23                            91 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           25                            89 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           25                            89 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           34                            80 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           34                            80 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         37                          77 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         37                          77 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           47                            67 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           47                            67 
[1] "DEL PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           27                            87 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           27                            87 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            58                             56 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            58                             56 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             64                              50 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             64                              50 
[1] "DEL PEAK 20(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            47                             67 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            47                             67 
[1] "DEL PEAK 21(11Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                            46                             68 
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                            46                             68 
[1] "DEL PEAK 22(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                            33                             81 
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                            33                             81 
[1] "DEL PEAK 23(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                          22                           92 
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                          22                           92 
[1] "DEL PEAK 24(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                            79                             35 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                            79                             35 
[1] "DEL PEAK 25(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                            37                             77 
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                            37                             77 
[1] "DEL PEAK 26(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                            19                             95 
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                            19                             95 
[1] "DEL PEAK 27(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                            63                             51 
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                            63                             51 
[1] "DEL PEAK 28(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                            64                             50 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                            64                             50 
[1] "DEL PEAK 29(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                            50                             64 
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                            50                             64 
[1] "DEL PEAK 30(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                            28                             86 
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                            28                             86 
[1] "DEL PEAK 31(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                            29                             85 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                            29                             85 
[1] "DEL PEAK 32(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          35                           79 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          35                           79 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            33                             81 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            33                             81 
[1] "DEL PEAK 34(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                             41                              73 
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                             41                              73 
[1] "DEL PEAK 35(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                            20                             94 
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                            20                             94 
[1] "DEL PEAK 36(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                            31                             83 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                            31                             83 
[1] "DEL PEAK 37(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                             38                              76 
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                             38                              76 
[1] "DEL PEAK 38(XP22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                            35                             79 
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                            35                             79 
[1] "DEL PEAK 39(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                           57                            57 
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                           57                            57 
[1] "DEL PEAK 40(XQ27.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                           57                            57 
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                           57                            57 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 114 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62          827           NA          745           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1291          960          908         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          261 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1620         1309           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3289          520          610          458          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1952           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
         828          455          805         2212          763          349 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
        1669          328          496           63          224           51 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
          NA           14            3            2            2          818 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
          NA          126           NA          729            3         1257 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
         298           NA          650          272           98           42 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
         217           NA           NA          966           NA         4362 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
        3555           NA         2229           NA          688          191 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
          NA           NA         2181         1107          356          160 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
          72           15          173          136          337            3 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
         124         2297           NA           NA           NA           NA 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
          NA           56           NA           NA          553          639 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
          NA          402           22           NA          826          259 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 114 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P32.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P32.1) MUTATED   22 14
  AMP PEAK  1(1P32.1) WILD-TYPE 56 22
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           36                            78 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           14                            22 
$`AMP PEAK  1(1P32.1) MUTATED`
TCGA-DX-A1L0 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ 
       18.54         5.26        76.41        66.87         6.28         8.58 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48K 
        9.70        23.08        70.49        42.77        14.99        19.30 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       24.26        26.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N9 
        7.36         0.46        26.89         4.57         4.14        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-KF-A41W 
        9.80        80.48         8.94        37.12         1.05        11.70 
TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-X6-A7WC 
        5.26         4.08         6.35        18.18         3.88        27.16 

$`AMP PEAK  1(1P32.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23Z TCGA-DX-A240 
       42.44        31.56        29.85        74.66        27.81        60.30 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       53.26        43.04         9.04       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88        64.18         9.73        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BH TCGA-DX-A6BK 
       14.96        72.72        25.08        11.47         1.68        16.18 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.10         0.07         0.07        12.62        23.97         0.10 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         3.22         1.38         7.13        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5Y9 
       22.62         6.28         3.91        71.70        36.39         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08        21.01        13.22         0.72        18.08         8.52 

  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                        80.48                        143.41 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                       13.345                        18.080 
[1] "0.5 - 80.5 (13.3)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.7"
D1V2, continuous
D1V3, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P32.1) MUTATED   18 18
  AMP PEAK  1(1P32.1) WILD-TYPE 44 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED     18   18
  AMP PEAK  1(1P32.1) WILD-TYPE   44   34
        clus
vv       AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE
  FEMALE                          18                            44
  MALE                            18                            34
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P32.1) MUTATED       0                         3    24
  AMP PEAK  1(1P32.1) WILD-TYPE     4                         5    53
D1V4, multiclass
                           clus
vv                          AMP PEAK  1(1P32.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              24
                           clus
vv                          AMP PEAK  1(1P32.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                53
[1] 3 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(1Q24.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q24.3) MUTATED   31 14
  AMP PEAK  2(1Q24.3) WILD-TYPE 47 22
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                           45                            69 
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                           14                            22 
$`AMP PEAK  2(1Q24.3) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23U 
       14.04        12.85        18.54        42.44        31.56        76.41 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 
       60.30         9.70        23.08        17.75        42.77        14.99 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
       28.80        64.18        19.30        12.26        27.22        26.47 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A48G TCGA-HB-A2OT 
        2.07         7.36         1.68         0.46         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       21.37         8.94         7.13        37.12        25.22       143.41 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-N1-A6IA TCGA-PC-A5DN TCGA-QQ-A5VC TCGA-SG-A6Z7 
       22.62         1.05         4.08        38.63        18.18         3.88 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
        0.72        18.08        27.16 

$`AMP PEAK  2(1Q24.3) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R 
        2.04        27.19        24.49        46.68        29.85        74.66 
TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 
        5.26        66.87         6.28        27.81         8.58        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       15.06         4.54        10.68        44.45        39.35        34.88 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
        9.73        24.26        14.96        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE 
       54.87        10.78        16.31        16.18         0.10         0.07 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AK TCGA-IS-A3K6 
        4.57        23.97         3.22         1.38        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        13.58        73.28         5.92         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47        11.08         0.10        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        6.35        81.01        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WD 
       21.01        13.22         8.52 

  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                       143.41                        116.88 
  AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE 
                        18.18                         16.31 
[1] "0.1 - 143.4 (18.2)" "0.1 - 116.9 (16.3)"
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q24.3) MUTATED   26 19
  AMP PEAK  2(1Q24.3) WILD-TYPE 36 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q24.3) MUTATED     26   19
  AMP PEAK  2(1Q24.3) WILD-TYPE   36   33
        clus
vv       AMP PEAK  2(1Q24.3) MUTATED AMP PEAK  2(1Q24.3) WILD-TYPE
  FEMALE                          26                            36
  MALE                            19                            33
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q24.3) MUTATED       2                         3    30
  AMP PEAK  2(1Q24.3) WILD-TYPE     2                         5    47
D2V4, multiclass
                           clus
vv                          AMP PEAK  2(1Q24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              30
                           clus
vv                          AMP PEAK  2(1Q24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                47
[1] 3 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(3P11.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(3P11.2) MUTATED   15 10
  AMP PEAK  3(3P11.2) WILD-TYPE 63 26
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                           25                            89 
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                           10                            26 
$`AMP PEAK  3(3P11.2) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT 
        2.04        12.85        74.66         6.28         9.04        23.08 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6BG TCGA-DX-A6BK 
       42.77         4.54        64.18        26.47         7.36        16.18 
TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IF-A4AK 
       26.89        80.48         8.94         3.22        25.22        31.76 
TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-UE-A6QU 
       11.70         4.47         6.35        18.08        46.82         0.72 
TCGA-X6-A7WC 
       27.16 

$`AMP PEAK  3(3P11.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU 
       60.30         8.58         9.70        53.26        43.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      108.13        17.10        20.05        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV 
        1.68         0.46         0.10         0.07         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         1.38         7.13        37.12        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       37.55        38.63        81.01         1.84        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01         3.88        13.22        18.08         8.52 

  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                         0.72                          0.07 
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                        80.48                        143.41 
  AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE 
                        16.18                         18.08 
[1] "0.7 - 80.5 (16.2)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK  3(3P11.2) MUTATED   12 13
  AMP PEAK  3(3P11.2) WILD-TYPE 50 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3P11.2) MUTATED     12   13
  AMP PEAK  3(3P11.2) WILD-TYPE   50   39
        clus
vv       AMP PEAK  3(3P11.2) MUTATED AMP PEAK  3(3P11.2) WILD-TYPE
  FEMALE                          12                            50
  MALE                            13                            39
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3P11.2) MUTATED       1                         2    17
  AMP PEAK  3(3P11.2) WILD-TYPE     3                         6    60
D3V4, multiclass
                           clus
vv                          AMP PEAK  3(3P11.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              17
                           clus
vv                          AMP PEAK  3(3P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                60
[1] 3 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(5P15.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(5P15.2) MUTATED   29 18
  AMP PEAK  4(5P15.2) WILD-TYPE 49 18
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                           47                            67 
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                           18                            18 
$`AMP PEAK  4(5P15.2) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3U7 TCGA-DX-A3U8 
       42.44        31.56         6.28         9.04        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R 
       14.99        28.80        64.18        24.26        14.96        26.47 
TCGA-DX-A6BA TCGA-DX-A6BG TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
       54.87         7.36        26.89         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
        0.10         8.94         3.22         7.13        25.22        31.76 
TCGA-IS-A3K6 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-LI-A67I TCGA-MJ-A68H 
       28.21         5.92         1.05        71.70         5.26         4.47 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        0.10         4.08         6.35        18.08        46.82        18.08 
TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.18         3.88        13.22         0.72        27.16 

$`AMP PEAK  4(5P15.2) WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       12.85        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
       17.75        10.68        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       19.30        12.26        27.22        72.72        25.08        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       10.78        16.31         2.07         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        0.10         0.07         0.07        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3K8 
       80.48        21.37         1.38        37.12       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        73.28        22.62         6.28         3.91        36.39 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-PC-A5DK 
       11.70         2.37         0.49         5.69        11.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-X6-A7WB 
       37.55        38.63        81.01         1.84        21.01        18.08 
TCGA-X6-A7WD 
        8.52 

  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                        71.70                        143.41 
  AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE 
                        14.96                         19.30 
[1] "0.1 - 71.7 (15.0)"  "0.1 - 143.4 (19.3)"
[1] "hr=" "2.3"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK  4(5P15.2) MUTATED   29 18
  AMP PEAK  4(5P15.2) WILD-TYPE 33 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5P15.2) MUTATED     29   18
  AMP PEAK  4(5P15.2) WILD-TYPE   33   34
        clus
vv       AMP PEAK  4(5P15.2) MUTATED AMP PEAK  4(5P15.2) WILD-TYPE
  FEMALE                          29                            33
  MALE                            18                            34
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5P15.2) MUTATED       3                         4    30
  AMP PEAK  4(5P15.2) WILD-TYPE     1                         4    47
D4V4, multiclass
                           clus
vv                          AMP PEAK  4(5P15.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              30
                           clus
vv                          AMP PEAK  4(5P15.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                47
[1] 3 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(6P21.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(6P21.1) MUTATED   16 10
  AMP PEAK  5(6P21.1) WILD-TYPE 62 26
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           26                            88 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           10                            26 
$`AMP PEAK  5(6P21.1) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3U9 
        2.04        27.19        42.44         6.28        70.49        14.99 
TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 
        1.68         0.46        26.89         4.57         0.10        41.33 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22         7.13       143.41        13.58         5.92         1.05 
TCGA-KF-A41W TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 
       11.70         5.26         4.08         6.35        38.63        46.82 
TCGA-QQ-A5VC TCGA-SG-A6Z7 
       18.18         3.88 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04        12.85        24.49        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BK 
       54.87        10.78        16.31         2.07         7.36        16.18 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07         0.07         4.14        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        21.37         8.94         1.38        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       25.22        31.76        28.21       116.88        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A5YA 
        6.28         3.91        71.70        36.39         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47        11.08         0.10        75.52        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT 
       81.01        18.08         1.84        18.08        21.01        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       143.41                        116.88 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                         6.74                         18.92 
[1] "0.1 - 143.4 (6.7)"  "0.1 - 116.9 (18.9)"
[1] "hr=" "1.8"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK  5(6P21.1) MUTATED   17  9
  AMP PEAK  5(6P21.1) WILD-TYPE 45 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     17    9
  AMP PEAK  5(6P21.1) WILD-TYPE   45   43
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                          17                            45
  MALE                             9                            43
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P21.1) MUTATED       0                         3    17
  AMP PEAK  5(6P21.1) WILD-TYPE     4                         5    60
D5V4, multiclass
                           clus
vv                          AMP PEAK  5(6P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              17
                           clus
vv                          AMP PEAK  5(6P21.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                60
[1] 3 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(6Q24.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(6Q24.3) MUTATED   22 10
  AMP PEAK  6(6Q24.3) WILD-TYPE 56 26
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           32                            82 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           10                            26 
$`AMP PEAK  6(6Q24.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L4 TCGA-DX-A23T 
        2.04        27.19        24.49        18.54        29.85         5.26 
TCGA-DX-A23Z TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       27.81        53.26        23.08        70.49        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A48N TCGA-DX-A6BH TCGA-DX-A6BK 
       15.06        17.75        14.99        12.26         1.68        16.18 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 
       26.89         4.57         4.14         3.22         7.13       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-PC-A5DL TCGA-PC-A5DM 
        5.92         1.05         5.26         2.37        37.55         6.35 
TCGA-QQ-A5VC TCGA-UE-A6QU 
       18.18         0.72 

$`AMP PEAK  6(6Q24.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R 
       14.04        12.85        46.68        42.44        31.56        74.66 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87         6.28        60.30         8.58         9.70 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       43.04         9.04       108.13        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A5W3 
        7.36         0.46         0.10         0.07         0.07        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         1.38        37.12        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        13.58        73.28        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       71.70        36.39        11.70         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       11.08         0.10         4.08        75.52        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 
       18.08         1.84        46.82        18.08        21.01         3.88 
TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22        18.08        27.16         8.52 

  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                         0.72                          0.07 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                       143.41                        116.88 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                        15.62                         18.69 
[1] "0.7 - 143.4 (15.6)" "0.1 - 116.9 (18.7)"
[1] "hr=" "1.3"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK  6(6Q24.3) MUTATED   14 18
  AMP PEAK  6(6Q24.3) WILD-TYPE 48 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q24.3) MUTATED     14   18
  AMP PEAK  6(6Q24.3) WILD-TYPE   48   34
        clus
vv       AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  FEMALE                          14                            48
  MALE                            18                            34
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6Q24.3) MUTATED       1                         2    21
  AMP PEAK  6(6Q24.3) WILD-TYPE     3                         6    56
D6V4, multiclass
                           clus
vv                          AMP PEAK  6(6Q24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              21
                           clus
vv                          AMP PEAK  6(6Q24.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(7Q31.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(7Q31.1) MUTATED   22  9
  AMP PEAK  7(7Q31.1) WILD-TYPE 56 27
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                           31                            83 
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                            9                            27 
$`AMP PEAK  7(7Q31.1) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y 
       27.19        12.85        24.49        46.68        42.44         6.28 
TCGA-DX-A23Z TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB 
       27.81        23.08        20.05        64.18        24.26        10.78 
TCGA-DX-A6BH TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 
        1.68         0.07        26.89         4.57         4.14         0.10 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-JV-A5VF 
        8.94         3.22         7.13        31.76        13.58         1.05 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU 
        2.37         0.10        37.55        18.08        18.18         0.72 
TCGA-X6-A7WC 
       27.16 

$`AMP PEAK  7(7Q31.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       14.04         2.04        18.54        31.56        29.85        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        66.87        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       15.06        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BK 
       11.47        54.87        16.31         2.07         7.36        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.46         0.10         0.07        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48        21.37         1.38        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        6.28         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01         3.88        13.22        18.08         8.52 

  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                        64.18                        143.41 
  AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE 
                        13.58                         18.08 
[1] "0.1 - 64.2 (13.6)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.4"
D7V2, continuous
D7V3, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q31.1) MUTATED   17 14
  AMP PEAK  7(7Q31.1) WILD-TYPE 45 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.1) MUTATED     17   14
  AMP PEAK  7(7Q31.1) WILD-TYPE   45   38
        clus
vv       AMP PEAK  7(7Q31.1) MUTATED AMP PEAK  7(7Q31.1) WILD-TYPE
  FEMALE                          17                            45
  MALE                            14                            38
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q31.1) MUTATED       2                         2    19
  AMP PEAK  7(7Q31.1) WILD-TYPE     2                         6    58
D7V4, multiclass
                           clus
vv                          AMP PEAK  7(7Q31.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              19
                           clus
vv                          AMP PEAK  7(7Q31.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                58
[1] 3 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(8Q21.12) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(8Q21.12) MUTATED   26 16
  AMP PEAK  8(8Q21.12) WILD-TYPE 52 20
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                            42                             72 
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                            16                             20 
$`AMP PEAK  8(8Q21.12) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R 
       14.04         2.04        12.85        24.49        42.44        74.66 
TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 
        5.26        27.81        20.05        15.06        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6BA TCGA-FX-A2QS 
       14.99        10.68        64.18        12.26        54.87         0.46 
TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.10         4.57         4.14         0.10        41.33        80.48 
TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        8.94        25.22        31.76        13.58         5.92         1.05 
TCGA-MB-A5Y9 TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        2.37         4.47        11.08         0.10         4.08        37.55 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.08        18.18         3.88        13.22         0.72        27.16 

$`AMP PEAK  8(8Q21.12) WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U 
       27.19        18.54        46.68        31.56        29.85        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3U6 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       17.75        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 
        1.68        16.18         0.07         0.07        26.89        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       23.97         9.80        21.37         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       37.12        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        6.28         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        0.49         5.69        75.52         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         1.84        46.82        21.01        18.08         8.52 

  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                         80.48                         143.41 
  AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE 
                        13.035                         21.190 
[1] "0.1 - 80.5 (13.0)"  "0.1 - 143.4 (21.2)"
[1] "hr=" "2.1"
D8V2, continuous
D8V3, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q21.12) MUTATED   23 19
  AMP PEAK  8(8Q21.12) WILD-TYPE 39 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q21.12) MUTATED     23   19
  AMP PEAK  8(8Q21.12) WILD-TYPE   39   33
        clus
vv       AMP PEAK  8(8Q21.12) MUTATED AMP PEAK  8(8Q21.12) WILD-TYPE
  FEMALE                           23                             39
  MALE                             19                             33
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q21.12) MUTATED       3                         4    25
  AMP PEAK  8(8Q21.12) WILD-TYPE     1                         4    52
D8V4, multiclass
                           clus
vv                          AMP PEAK  8(8Q21.12) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               25
                           clus
vv                          AMP PEAK  8(8Q21.12) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(11Q22.2) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(11Q22.2) MUTATED   12  5
  AMP PEAK  9(11Q22.2) WILD-TYPE 66 31
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                            17                             97 
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                             5                             31 
$`AMP PEAK  9(11Q22.2) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A2J1 
       27.19        46.68        42.44         5.26        27.81        53.26 
TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-HB-A43Z 
       23.08        20.05        19.30        24.26        12.26         4.14 
TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-KF-A41W TCGA-PC-A5DP TCGA-QQ-A5VA 
        0.10        21.37        11.70        18.08        18.08 

$`AMP PEAK  9(11Q22.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04         2.04        12.85        24.49        18.54        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 
       29.85        74.66        76.41        66.87         6.28        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58         9.70        43.04         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
        9.73        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC 
        6.35        38.63        81.01         1.84        46.82        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       21.01         3.88        13.22         0.72        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                         53.26                         143.41 
  AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE 
                         20.05                          16.18 
[1] "0.1 - 53.3 (20.1)"  "0.1 - 143.4 (16.2)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  AMP PEAK  9(11Q22.2) MUTATED    9  8
  AMP PEAK  9(11Q22.2) WILD-TYPE 53 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11Q22.2) MUTATED      9    8
  AMP PEAK  9(11Q22.2) WILD-TYPE   53   44
        clus
vv       AMP PEAK  9(11Q22.2) MUTATED AMP PEAK  9(11Q22.2) WILD-TYPE
  FEMALE                            9                             53
  MALE                              8                             44
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(11Q22.2) MUTATED       0                         0    10
  AMP PEAK  9(11Q22.2) WILD-TYPE     4                         8    67
D9V4, multiclass
                           clus
vv                          AMP PEAK  9(11Q22.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          AMP PEAK  9(11Q22.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(12P13.32) MUTATION ANALYSIS
D10V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 10(12P13.32) MUTATED   12  9
  AMP PEAK 10(12P13.32) WILD-TYPE 66 27
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                             21                              93 
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                              9                              27 
$`AMP PEAK 10(12P13.32) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LY 
       14.04        27.19        12.85        53.26         9.04        17.10 
TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6BK TCGA-FX-A48G TCGA-HB-A3YV 
       15.06        12.26        26.47        16.18         0.07         4.57 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-MB-A5Y9 TCGA-MB-A8JL 
       25.22       143.41         5.92         6.28         2.37         5.69 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA 
        0.10        37.55        18.08 

$`AMP PEAK 10(12P13.32) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        24.49        18.54        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LT 
       27.81        60.30         8.58         9.70        43.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        20.05        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        2.07         7.36         1.68         0.46         0.10         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       26.89         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        7.13        37.12        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA 
       11.70         5.26         0.49         4.47        11.08         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                         143.41                          116.88 
  AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE 
                          14.04                           18.54 
[1] "0.1 - 143.4 (14.0)" "0.1 - 116.9 (18.5)"
[1] "hr=" "1.9"
D10V2, continuous
D10V3, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P13.32) MUTATED   10 11
  AMP PEAK 10(12P13.32) WILD-TYPE 52 41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.32) MUTATED     10   11
  AMP PEAK 10(12P13.32) WILD-TYPE   52   41
        clus
vv       AMP PEAK 10(12P13.32) MUTATED AMP PEAK 10(12P13.32) WILD-TYPE
  FEMALE                            10                              52
  MALE                              11                              41
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12P13.32) MUTATED       1                         1    16
  AMP PEAK 10(12P13.32) WILD-TYPE     3                         7    61
D10V4, multiclass
                           clus
vv                          AMP PEAK 10(12P13.32) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                16
                           clus
vv                          AMP PEAK 10(12P13.32) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                  61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(12P12.1) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(12P12.1) MUTATED   14 11
  AMP PEAK 11(12P12.1) WILD-TYPE 64 25
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            25                             89 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            11                             25 
$`AMP PEAK 11(12P12.1) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LS 
       14.04        27.19        12.85        24.49        74.66         9.04 
TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A48N TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 
       17.10        42.77        12.26         4.57         0.10        41.33 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-MB-A5Y9 TCGA-MB-A8JL 
        3.22        25.22         5.92         6.28         2.37         5.69 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        0.10        37.55        38.63        81.01        46.82        18.08 
TCGA-QQ-A5VC 
       18.18 

$`AMP PEAK 11(12P12.1) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        18.54        46.68        42.44        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58         9.70        53.26        43.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
      108.13        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        80.48        21.37         8.94         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA 
       11.70         5.26         0.49         4.47        11.08         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-SG-A6Z7 
       75.52         6.35        18.08         1.84        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                         81.01                         143.41 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                         17.10                          18.08 
[1] "0.1 - 81.0 (17.1)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.6"
D11V2, continuous
D11V3, binary
                                cls
clus                              0  1
  AMP PEAK 11(12P12.1) MUTATED   14 11
  AMP PEAK 11(12P12.1) WILD-TYPE 48 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     14   11
  AMP PEAK 11(12P12.1) WILD-TYPE   48   41
        clus
vv       AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  FEMALE                           14                             48
  MALE                             11                             41
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P12.1) MUTATED       1                         1    17
  AMP PEAK 11(12P12.1) WILD-TYPE     3                         7    60
D11V4, multiclass
                           clus
vv                          AMP PEAK 11(12P12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               17
                           clus
vv                          AMP PEAK 11(12P12.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 60
[1] 3 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(12Q15) MUTATION ANALYSIS
D12V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 12(12Q15) MUTATED   31 15
  AMP PEAK 12(12Q15) WILD-TYPE 47 21
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          46                           68 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                          15                           21 
$`AMP PEAK 12(12Q15) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V 
       42.44        31.56        29.85        74.66         5.26        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF 
       20.05        15.06        17.75        12.26        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 
        7.36         1.68         0.46         4.57         0.10        41.33 
TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN 
        3.22        37.12        11.70         0.10        37.55        38.63 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QU 
       18.08        18.18         3.88         0.72 

$`AMP PEAK 12(12Q15) WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A23U TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       27.19        76.41        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BK TCGA-FX-A3NJ 
       25.08        11.47        54.87        10.78        16.18         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        80.48        21.37         8.94         1.38         7.13 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DO 
        4.47        11.08         4.08        75.52         6.35        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB 
       18.08         1.84        46.82        21.01        13.22        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                      108.13                       143.41 
  AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE 
                      17.425                       18.080 
[1] "0.1 - 108.1 (17.4)" "0.1 - 143.4 (18.1)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                              cls
clus                            0  1
  AMP PEAK 12(12Q15) MUTATED   19 27
  AMP PEAK 12(12Q15) WILD-TYPE 43 25
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 12(12Q15) MUTATED     19   27
  AMP PEAK 12(12Q15) WILD-TYPE   43   25
        clus
vv       AMP PEAK 12(12Q15) MUTATED AMP PEAK 12(12Q15) WILD-TYPE
  FEMALE                         19                           43
  MALE                           27                           25
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12Q15) MUTATED       2                         0    24
  AMP PEAK 12(12Q15) WILD-TYPE     2                         8    53
D12V4, multiclass
                           clus
vv                          AMP PEAK 12(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             24
                           clus
vv                          AMP PEAK 12(12Q15) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               53
[1] 3 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(13Q34) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 13(13Q34) MUTATED   11  8
  AMP PEAK 13(13Q34) WILD-TYPE 67 28
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                          19                           95 
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                           8                           28 
$`AMP PEAK 13(13Q34) MUTATED`
TCGA-DX-A23R TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6BB TCGA-DX-A6BK 
       74.66        14.99        24.26        12.26        10.78        16.18 
TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VE 
       41.33         7.13        31.76       143.41        13.58         6.28 
TCGA-KF-A41W TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP 
       11.70         4.47         4.08        37.55         6.35        18.08 
TCGA-X6-A7WB 
       18.08 

$`AMP PEAK 13(13Q34) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        19.30        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        54.87        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        1.68         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       80.48        21.37         8.94         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       25.22        28.21       116.88        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
        0.49         5.69        11.08         0.10        75.52        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01         1.84        46.82        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22         0.72        27.16         8.52 

  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                        4.08                         0.07 
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                      143.41                       116.88 
  AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE 
                       14.99                        18.18 
[1] "4.1 - 143.4 (15.0)" "0.1 - 116.9 (18.2)"
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
                              cls
clus                            0  1
  AMP PEAK 13(13Q34) MUTATED   14  5
  AMP PEAK 13(13Q34) WILD-TYPE 48 47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(13Q34) MUTATED     14    5
  AMP PEAK 13(13Q34) WILD-TYPE   48   47
        clus
vv       AMP PEAK 13(13Q34) MUTATED AMP PEAK 13(13Q34) WILD-TYPE
  FEMALE                         14                           48
  MALE                            5                           47
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(13Q34) MUTATED       0                         3    14
  AMP PEAK 13(13Q34) WILD-TYPE     4                         5    63
D13V4, multiclass
                           clus
vv                          AMP PEAK 13(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             14
                           clus
vv                          AMP PEAK 13(13Q34) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               63
[1] 3 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(17P11.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(17P11.2) MUTATED   24 14
  AMP PEAK 14(17P11.2) WILD-TYPE 54 22
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                            38                             76 
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                            14                             22 
$`AMP PEAK 14(17P11.2) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U5 TCGA-DX-A3UC 
        2.04        12.85        42.44         6.28        15.06        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA 
       34.88        64.18        19.30        24.26        26.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
       10.78        16.18         0.07         0.07         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
       23.97        41.33        21.37         3.22         7.13        25.22 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-KF-A41W TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA 
        3.91        71.70        11.70         5.26         0.10         4.08 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QU 
        6.35        81.01        18.08        46.82        18.08         0.72 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

$`AMP PEAK 14(17P11.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04        27.19        24.49        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 
       23.08        70.49       108.13        17.10        20.05        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD 
       42.77         4.54        14.99        10.68        44.45        28.80 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
        9.73        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS 
       11.47        16.31         2.07         7.36         1.68         0.46 
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        0.10        26.89         4.14         0.10         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        8.94         1.38        37.12        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
        1.05        36.39         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VC 
       11.08        75.52        37.55        38.63         1.84        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       21.01         3.88        13.22        18.08 

  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                         81.01                         143.41 
  AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE 
                         15.62                          18.13 
[1] "0.1 - 81.0 (15.6)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.5"
D14V2, continuous
D14V3, binary
                                cls
clus                              0  1
  AMP PEAK 14(17P11.2) MUTATED   25 13
  AMP PEAK 14(17P11.2) WILD-TYPE 37 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(17P11.2) MUTATED     25   13
  AMP PEAK 14(17P11.2) WILD-TYPE   37   39
        clus
vv       AMP PEAK 14(17P11.2) MUTATED AMP PEAK 14(17P11.2) WILD-TYPE
  FEMALE                           25                             37
  MALE                             13                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(17P11.2) MUTATED       2                         1    29
  AMP PEAK 14(17P11.2) WILD-TYPE     2                         7    48
D14V4, multiclass
                           clus
vv                          AMP PEAK 14(17P11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               29
                           clus
vv                          AMP PEAK 14(17P11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 48
[1] 3 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(17Q24.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(17Q24.3) MUTATED   19 10
  AMP PEAK 15(17Q24.3) WILD-TYPE 59 26
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                            29                             85 
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                            10                             26 
$`AMP PEAK 15(17Q24.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48K 
        2.04        42.44         9.70        20.05        10.68        19.30 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        2.07        16.18         0.46         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ 
        4.57         4.14        12.62         0.10        41.33         7.13 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA 
       13.58        73.28         3.91         5.26         0.10         4.08 
TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QU 
       18.08        18.08        18.18         3.88         0.72 

$`AMP PEAK 15(17Q24.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         8.58        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 
        9.04        23.08        70.49       108.13        17.10        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88        64.18         9.73        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ 
       54.87        10.78        16.31         7.36         1.68         0.10 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       23.97         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
      116.88         5.92        22.62         6.28         1.05        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39        11.70         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       11.08        75.52        37.55         6.35        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
        1.84        46.82        21.01        13.22        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                         73.28                         143.41 
  AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE 
                          7.13                          23.08 
[1] "0.1 - 73.3 (7.1)"   "0.1 - 143.4 (23.1)"
[1] "hr=" "2.6"
D15V2, continuous
D15V3, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q24.3) MUTATED   23  6
  AMP PEAK 15(17Q24.3) WILD-TYPE 39 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q24.3) MUTATED     23    6
  AMP PEAK 15(17Q24.3) WILD-TYPE   39   46
        clus
vv       AMP PEAK 15(17Q24.3) MUTATED AMP PEAK 15(17Q24.3) WILD-TYPE
  FEMALE                           23                             39
  MALE                              6                             46
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(17Q24.3) MUTATED       2                         2    20
  AMP PEAK 15(17Q24.3) WILD-TYPE     2                         6    57
D15V4, multiclass
                           clus
vv                          AMP PEAK 15(17Q24.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               20
                           clus
vv                          AMP PEAK 15(17Q24.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(19P13.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 16(19P13.2) MUTATED   28 11
  AMP PEAK 16(19P13.2) WILD-TYPE 50 25
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                            39                             75 
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                            11                             25 
$`AMP PEAK 16(19P13.2) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LW 
       42.44        31.56        74.66         6.28         9.70       108.13 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B9 
       42.77        14.99        28.80        64.18        12.26        11.47 
TCGA-DX-A6BA TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA 
       54.87         0.07         0.07         4.57        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-JV-A75J TCGA-MB-A5YA 
       80.48         8.94         3.22         1.38         3.91         0.49 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QT 
        4.47         4.08        46.82        18.08        18.18        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
        0.72        18.08        27.16 

$`AMP PEAK 16(19P13.2) WILD-TYPE`
TCGA-DX-A1L0 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       18.54        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         8.58        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       70.49        17.10        20.05        15.06        17.75         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.46         0.10        26.89         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        0.10        21.37         7.13        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         1.05        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        5.26         2.37         5.69        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       37.55         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WD 
       21.01         3.88         8.52 

  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                        108.13                         143.41 
  AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE 
                         14.04                          18.54 
[1] "0.1 - 108.1 (14.0)" "0.1 - 143.4 (18.5)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                                cls
clus                              0  1
  AMP PEAK 16(19P13.2) MUTATED   20 19
  AMP PEAK 16(19P13.2) WILD-TYPE 42 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(19P13.2) MUTATED     20   19
  AMP PEAK 16(19P13.2) WILD-TYPE   42   33
        clus
vv       AMP PEAK 16(19P13.2) MUTATED AMP PEAK 16(19P13.2) WILD-TYPE
  FEMALE                           20                             42
  MALE                             19                             33
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(19P13.2) MUTATED       2                         3    22
  AMP PEAK 16(19P13.2) WILD-TYPE     2                         5    55
D16V4, multiclass
                           clus
vv                          AMP PEAK 16(19P13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               22
                           clus
vv                          AMP PEAK 16(19P13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(19Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 17(19Q12) MUTATED   25 12
  AMP PEAK 17(19Q12) WILD-TYPE 53 24
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          37                           77 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          12                           24 
$`AMP PEAK 17(19Q12) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        27.19        12.85        46.68        42.44 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       74.66         6.28        23.08        42.77        14.99        39.35 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B9 TCGA-FX-A2QS 
       64.18        19.30        12.26        26.47        11.47         0.46 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        12.62         0.10         9.80         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-KF-A41W 
        1.38         7.13        13.58         5.92         1.05        11.70 
TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU 
        5.26         6.35        18.08        18.08        18.18         0.72 
TCGA-X6-A7WC 
       27.16 

$`AMP PEAK 17(19Q12) WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       24.49        18.54        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD 
       15.06        17.75         4.54        10.68        44.45        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       34.88         9.73        24.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        1.68        16.18         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A3RQ 
        4.14        23.97        41.33        80.48        21.37        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       25.22        31.76        28.21       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5Y9 
       22.62         6.28         3.91        71.70        36.39         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52        37.55        38.63        81.01         1.84        46.82 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01         3.88        13.22        18.08         8.52 

  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                       74.66                       143.41 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                       12.62                        21.37 
[1] "0.1 - 74.7 (12.6)"  "0.1 - 143.4 (21.4)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED   21 16
  AMP PEAK 17(19Q12) WILD-TYPE 41 36
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED     21   16
  AMP PEAK 17(19Q12) WILD-TYPE   41   36
        clus
vv       AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  FEMALE                         21                           41
  MALE                           16                           36
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(19Q12) MUTATED       1                         2    25
  AMP PEAK 17(19Q12) WILD-TYPE     3                         6    52
D17V4, multiclass
                           clus
vv                          AMP PEAK 17(19Q12) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             25
                           clus
vv                          AMP PEAK 17(19Q12) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(20Q13.33) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 18(20Q13.33) MUTATED   27 15
  AMP PEAK 18(20Q13.33) WILD-TYPE 51 21
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                             42                              72 
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                             15                              21 
$`AMP PEAK 18(20Q13.33) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LW 
       46.68        42.44        74.66         6.28         8.58       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48V 
       15.06        14.99        10.68        12.26        14.96        25.08 
TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI 
       10.78         0.10         0.07         4.57        80.48         8.94 
TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
        3.22        31.76       143.41        13.58         5.92         6.28 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
       11.70         5.26         2.37         4.08        37.55         6.35 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       46.82        18.08        21.01         0.72        18.08        27.16 

$`AMP PEAK 18(20Q13.33) WILD-TYPE`
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49        17.10        20.05        17.75        42.77         4.54 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 
       19.30        24.26        27.22        26.47        72.72        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       54.87        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.46         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.10        41.33         9.80        21.37         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       37.12        25.22        28.21       116.88        73.28        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL 
        1.05         3.91        71.70        36.39         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
        4.47        11.08         0.10        75.52        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WD 
       18.08         1.84        18.18         3.88        13.22         8.52 

  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                         143.41                          116.88 
  AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE 
                          13.81                           20.71 
[1] "0.1 - 143.4 (13.8)" "0.1 - 116.9 (20.7)"
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
                                 cls
clus                               0  1
  AMP PEAK 18(20Q13.33) MUTATED   18 24
  AMP PEAK 18(20Q13.33) WILD-TYPE 44 28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20Q13.33) MUTATED     18   24
  AMP PEAK 18(20Q13.33) WILD-TYPE   44   28
        clus
vv       AMP PEAK 18(20Q13.33) MUTATED AMP PEAK 18(20Q13.33) WILD-TYPE
  FEMALE                            18                              44
  MALE                              24                              28
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(20Q13.33) MUTATED       1                         2    29
  AMP PEAK 18(20Q13.33) WILD-TYPE     3                         6    48
D18V4, multiclass
                           clus
vv                          AMP PEAK 18(20Q13.33) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                29
                           clus
vv                          AMP PEAK 18(20Q13.33) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  48
[1] 3 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(21Q21.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(21Q21.1) MUTATED   21 12
  AMP PEAK 19(21Q21.1) WILD-TYPE 57 24
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                            33                             81 
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                            12                             24 
$`AMP PEAK 19(21Q21.1) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A23T TCGA-DX-A23U 
        2.04        27.19        12.85        46.68         5.26        76.41 
TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A6BB 
        8.58       108.13        14.99        64.18        19.30        10.78 
TCGA-DX-A6BF TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ 
        2.07         4.57         0.10        41.33        80.48         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA 
        7.13        25.22        13.58        11.70         5.26         0.49 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-QQ-A5VC 
        4.47         4.08        37.55         6.35        46.82        18.18 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
        3.88        13.22        27.16 

$`AMP PEAK 19(21Q21.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        24.49        18.54        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       74.66        66.87         6.28        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       53.26        43.04         9.04        23.08        70.49        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L 
       44.45        39.35        28.80        34.88         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        54.87        16.31         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z 
        0.46         0.10         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       12.62        23.97         9.80        21.37         8.94         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        31.76        28.21       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
       36.39         2.37         5.69        11.08         0.10        75.52 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD 
       38.63        81.01        18.08         1.84        18.08        21.01 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
        0.72        18.08         8.52 

  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                        108.13                         143.41 
  AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE 
                         12.85                          18.54 
[1] "0.1 - 108.1 (12.8)" "0.1 - 143.4 (18.5)"
[1] "hr=" "1.4"
D19V2, continuous
D19V3, binary
                                cls
clus                              0  1
  AMP PEAK 19(21Q21.1) MUTATED   16 17
  AMP PEAK 19(21Q21.1) WILD-TYPE 46 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(21Q21.1) MUTATED     16   17
  AMP PEAK 19(21Q21.1) WILD-TYPE   46   35
        clus
vv       AMP PEAK 19(21Q21.1) MUTATED AMP PEAK 19(21Q21.1) WILD-TYPE
  FEMALE                           16                             46
  MALE                             17                             35
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(21Q21.1) MUTATED       1                         2    21
  AMP PEAK 19(21Q21.1) WILD-TYPE     3                         6    56
D19V4, multiclass
                           clus
vv                          AMP PEAK 19(21Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               21
                           clus
vv                          AMP PEAK 19(21Q21.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(XP21.2) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 20(XP21.2) MUTATED   23 13
  AMP PEAK 20(XP21.2) WILD-TYPE 55 23
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                           36                            78 
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                           13                            23 
$`AMP PEAK 20(XP21.2) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A240 TCGA-DX-A3LW 
       27.19        12.85        24.49        18.54        60.30       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE 
       17.10        20.05         4.54        10.68        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A2QS TCGA-HB-A2OT 
       64.18        24.26        54.87        10.78         0.46        26.89 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ 
        4.57        23.97        41.33        80.48         8.94         7.13 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-MJ-A68H TCGA-N1-A6IA 
       37.12        28.21        13.58        22.62         4.47         4.08 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5VC TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        6.35        38.63        18.18         0.72        27.16         8.52 

$`AMP PEAK 20(XP21.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        46.68        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB 
       70.49        15.06        17.75        42.77        14.99        44.45 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       28.80         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
       26.47        72.72        25.08        11.47        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        7.36         1.68        16.18         0.10         0.07         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ 
        4.14        12.62         0.10         9.80        21.37         3.22 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
        1.38        25.22        31.76       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92         6.28         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         5.69        11.08 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
        0.10        75.52        37.55        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       46.82        18.08        21.01         3.88        13.22        18.08 

  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                       108.13                        143.41 
  AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE 
                       21.335                        15.620 
[1] "0.5 - 108.1 (21.3)" "0.1 - 143.4 (15.6)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                               cls
clus                             0  1
  AMP PEAK 20(XP21.2) MUTATED   23 13
  AMP PEAK 20(XP21.2) WILD-TYPE 39 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(XP21.2) MUTATED     23   13
  AMP PEAK 20(XP21.2) WILD-TYPE   39   39
        clus
vv       AMP PEAK 20(XP21.2) MUTATED AMP PEAK 20(XP21.2) WILD-TYPE
  FEMALE                          23                            39
  MALE                            13                            39
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(XP21.2) MUTATED       2                         3    23
  AMP PEAK 20(XP21.2) WILD-TYPE     2                         5    54
D20V4, multiclass
                           clus
vv                          AMP PEAK 20(XP21.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              23
                           clus
vv                          AMP PEAK 20(XP21.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(XQ21.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 21(XQ21.2) MUTATED    7 11
  AMP PEAK 21(XQ21.2) WILD-TYPE 71 25
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                           18                            96 
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                           11                            25 
$`AMP PEAK 21(XQ21.2) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LY 
       12.85        24.49        18.54        46.68         6.28        17.10 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-JV-A75J 
       41.33         8.94        37.12        28.21        13.58         3.91 
TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-X6-A7WC 
        5.26         6.35        81.01        18.08         3.88        27.16 

$`AMP PEAK 21(XQ21.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        27.19        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       70.49       108.13        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        21.37         3.22         1.38         7.13        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       31.76       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 
        6.28         1.05        71.70        36.39        11.70         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52        37.55        38.63        18.08         1.84        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       18.18        21.01        13.22         0.72        18.08         8.52 

  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                         3.88                          0.07 
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                        81.01                        143.41 
  AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE 
                       17.590                        17.915 
[1] "3.9 - 81.0 (17.6)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "2.4"
D21V2, continuous
D21V3, binary
                               cls
clus                             0  1
  AMP PEAK 21(XQ21.2) MUTATED   10  8
  AMP PEAK 21(XQ21.2) WILD-TYPE 52 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(XQ21.2) MUTATED     10    8
  AMP PEAK 21(XQ21.2) WILD-TYPE   52   44
        clus
vv       AMP PEAK 21(XQ21.2) MUTATED AMP PEAK 21(XQ21.2) WILD-TYPE
  FEMALE                          10                            52
  MALE                             8                            44
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(XQ21.2) MUTATED       0                         0    12
  AMP PEAK 21(XQ21.2) WILD-TYPE     4                         8    65
D21V4, multiclass
                           clus
vv                          AMP PEAK 21(XQ21.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              12
                           clus
vv                          AMP PEAK 21(XQ21.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.32) MUTATED   29  7
  DEL PEAK  1(1P36.32) WILD-TYPE 49 29
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            36                             78 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             7                             29 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-DX-A1KX TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       27.19       108.13        15.06        42.77        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       39.35        64.18         9.73        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3RE TCGA-FX-A48G 
       72.72        25.08        54.87        10.78         0.07         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK 
        4.14        12.62         0.10         9.80        21.37         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        31.76       143.41       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-X6-A7WD 
       22.62         4.47         0.10        75.52        37.55         8.52 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       53.26        43.04         9.04        23.08        70.49        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       20.05        17.75         4.54        44.45        28.80        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
       19.30        24.26        12.26        11.47        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT 
        7.36         1.68        16.18         0.46         0.10        26.89 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        23.97        41.33        80.48         8.94         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
        7.13        25.22        28.21         5.92         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
        3.91        71.70        36.39        11.70         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN 
        0.49         5.69        11.08         4.08         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       21.01         3.88        13.22         0.72        18.08        27.16 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.07                           0.10 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        143.41                          81.01 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        21.995                         17.425 
[1] "0.1 - 143.4 (22.0)" "0.1 - 81.0 (17.4)" 
[1] "hr=" "2.6"
D22V2, continuous
D22V3, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED   24 12
  DEL PEAK  1(1P36.32) WILD-TYPE 38 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     24   12
  DEL PEAK  1(1P36.32) WILD-TYPE   38   40
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           24                             38
  MALE                             12                             40
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       2                         2    29
  DEL PEAK  1(1P36.32) WILD-TYPE     2                         6    48
D22V4, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               29
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 48
[1] 3 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 = DEL PEAK  2(1P32.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P32.3) MUTATED   16  2
  DEL PEAK  2(1P32.3) WILD-TYPE 62 34
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                           18                            96 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                            2                            34 
$`DEL PEAK  2(1P32.3) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A3LY TCGA-DX-A3UA TCGA-DX-A3UF 
       27.19        46.68        42.44        17.10        10.68        64.18 
TCGA-DX-A6B9 TCGA-FX-A3RE TCGA-FX-A48G TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       11.47         0.07         0.07       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-MO-A47R TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
       73.28        22.62         0.10         0.72        27.16         8.52 

$`DEL PEAK  2(1P32.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04         2.04        12.85        24.49        18.54        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49       108.13        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BA 
       27.22        14.96        26.47        72.72        25.08        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.46         0.10        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       31.76        28.21         5.92         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47        11.08         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       18.08        18.18        21.01         3.88        13.22        18.08 

  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       143.41                        108.13 
  DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE 
                       19.860                        17.915 
[1] "0.1 - 143.4 (19.9)" "0.1 - 108.1 (17.9)"
[1] "hr=" "4.2"
D23V2, continuous
D23V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P32.3) MUTATED   14  4
  DEL PEAK  2(1P32.3) WILD-TYPE 48 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P32.3) MUTATED     14    4
  DEL PEAK  2(1P32.3) WILD-TYPE   48   48
        clus
vv       DEL PEAK  2(1P32.3) MUTATED DEL PEAK  2(1P32.3) WILD-TYPE
  FEMALE                          14                            48
  MALE                             4                            48
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P32.3) MUTATED       3                         1    11
  DEL PEAK  2(1P32.3) WILD-TYPE     1                         7    66
D23V4, multiclass
                           clus
vv                          DEL PEAK  2(1P32.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              11
                           clus
vv                          DEL PEAK  2(1P32.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q44) MUTATED   20 11
  DEL PEAK  3(1Q44) WILD-TYPE 58 25
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         31                          83 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         11                          25 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.54        46.68        42.44 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A48J TCGA-DX-A6BA 
      108.13        17.10        15.06        42.77         9.73        54.87 
TCGA-DX-A6BF TCGA-FX-A2QS TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 
        2.07         0.46         0.07        26.89         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA 
       23.97         9.80         3.22         7.13        37.12        13.58 
TCGA-KF-A41W TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-SG-A6Z7 
       11.70         4.08         6.35        81.01        18.08         3.88 
TCGA-X6-A7WD 
        8.52 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       14.04         2.04        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       20.05        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       39.35        28.80        34.88        64.18        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.10         0.07         4.14         0.10        41.33        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37         8.94         1.38        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       37.55        38.63         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       21.01        13.22         0.72        18.08        27.16 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                     108.13                      143.41 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      13.58                       18.18 
[1] "0.1 - 108.1 (13.6)" "0.1 - 143.4 (18.2)"
[1] "hr=" "1.3"
D24V2, continuous
D24V3, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED   19 12
  DEL PEAK  3(1Q44) WILD-TYPE 43 40
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     19   12
  DEL PEAK  3(1Q44) WILD-TYPE   43   40
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        19                          43
  MALE                          12                          40
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED       0                         3    20
  DEL PEAK  3(1Q44) WILD-TYPE     4                         5    57
D24V4, multiclass
                           clus
vv                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            20
                           clus
vv                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = DEL PEAK  4(2P25.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2P25.3) MUTATED   28 10
  DEL PEAK  4(2P25.3) WILD-TYPE 50 26
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                           38                            76 
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                           10                            26 
$`DEL PEAK  4(2P25.3) MUTATED`
TCGA-DX-A1L2 TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       42.44        17.10        20.05        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V 
       34.88        64.18        24.26        27.22        14.96        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z 
       11.47        54.87         2.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ 
       12.62        23.97         0.10        41.33         3.22         7.13 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        31.76        13.58        73.28        22.62         6.28 
TCGA-K1-A3PN TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 
       71.70         4.47         4.08        81.01        18.08        46.82 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

$`DEL PEAK  4(2P25.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       46.68        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        10.68        44.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BB 
        9.73        19.30        12.26        26.47        72.72        10.78 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
       16.31         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.07         4.57         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 
        1.38        37.12        28.21       143.41       116.88         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        36.39        11.70         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        0.49         5.69        11.08         0.10        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
        6.35        38.63         1.84        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
        3.88        13.22         0.72        27.16 

  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                        81.01                        143.41 
  DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE 
                       21.335                        15.620 
[1] "0.1 - 81.0 (21.3)"  "0.1 - 143.4 (15.6)"
[1] "hr=" "1.4"
D25V2, continuous
D25V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(2P25.3) MUTATED   30  8
  DEL PEAK  4(2P25.3) WILD-TYPE 32 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2P25.3) MUTATED     30    8
  DEL PEAK  4(2P25.3) WILD-TYPE   32   44
        clus
vv       DEL PEAK  4(2P25.3) MUTATED DEL PEAK  4(2P25.3) WILD-TYPE
  FEMALE                          30                            32
  MALE                             8                            44
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P25.3) MUTATED       1                         5    28
  DEL PEAK  4(2P25.3) WILD-TYPE     3                         3    49
D25V4, multiclass
                           clus
vv                          DEL PEAK  4(2P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              28
                           clus
vv                          DEL PEAK  4(2P25.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q37.3) MUTATED   23 18
  DEL PEAK  5(2Q37.3) WILD-TYPE 55 18
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           41                            73 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           18                            18 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M1 
       12.85        18.54        46.68        42.44         6.28        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF 
       15.06        42.77        14.99        10.68        28.80        64.18 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A48G 
       24.26        26.47        25.08         2.07        16.18         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       26.89         4.57        41.33         9.80        80.48        21.37 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M6 
        3.22         7.13        37.12        28.21        13.58        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO TCGA-KF-A41W TCGA-N1-A6IA TCGA-PC-A5DM 
        6.28         1.05        36.39        11.70         4.08         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WD 
       81.01        18.08         3.88        18.08         8.52 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        27.19        24.49        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       70.49       108.13        17.10        17.75         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       39.35        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        11.47        54.87        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A43Z 
        7.36         1.68         0.46         0.10         0.07         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       12.62        23.97         0.10         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A75J 
       31.76       143.41       116.88        73.28         5.92         3.91 
TCGA-K1-A3PN TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       71.70         5.26         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 
       11.08         0.10        75.52        37.55        38.63         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.08        18.18        21.01        13.22         0.72 
TCGA-X6-A7WC 
       27.16 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        81.01                        143.41 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        18.08                         17.75 
[1] "0.1 - 81.0 (18.1)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "2"  
D26V2, continuous
D26V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   25 16
  DEL PEAK  5(2Q37.3) WILD-TYPE 37 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     25   16
  DEL PEAK  5(2Q37.3) WILD-TYPE   37   36
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                          25                            37
  MALE                            16                            36
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED       1                         4    29
  DEL PEAK  5(2Q37.3) WILD-TYPE     3                         4    48
D26V4, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              29
                           clus
vv                          DEL PEAK  5(2Q37.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                48
[1] 3 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 = DEL PEAK  6(2Q37.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(2Q37.3) MUTATED   25 18
  DEL PEAK  6(2Q37.3) WILD-TYPE 53 18
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                           43                            71 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                           18                            18 
$`DEL PEAK  6(2Q37.3) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LW 
       12.85        18.54        46.68        42.44         6.28       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE 
       20.05        15.06        42.77        14.99        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A3RE 
       64.18        26.47        25.08         2.07        16.18         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        0.07        26.89         4.57        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         3.22         7.13        37.12        28.21       143.41 
TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W 
       13.58        22.62         6.28         1.05         3.91        11.70 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-SG-A6Z7 TCGA-X6-A7WB 
        4.08         6.35        81.01        18.08         3.88        18.08 
TCGA-X6-A7WD 
        8.52 

$`DEL PEAK  6(2Q37.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        27.19        24.49        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       70.49        17.10        17.75         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       39.35         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        11.47        54.87        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A43Z TCGA-HB-A5W3 
        7.36         1.68         0.46         0.10         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       23.97         0.10         8.94         1.38        25.22        31.76 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
      116.88        73.28         5.92        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       75.52        37.55        38.63         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.18        21.01        13.22         0.72        27.16 

  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                        18.08                         17.75 
[1] "0.1 - 143.4 (18.1)" "0.1 - 116.9 (17.8)"
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(2Q37.3) MUTATED   27 16
  DEL PEAK  6(2Q37.3) WILD-TYPE 35 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.3) MUTATED     27   16
  DEL PEAK  6(2Q37.3) WILD-TYPE   35   36
        clus
vv       DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  FEMALE                          27                            35
  MALE                            16                            36
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q37.3) MUTATED       1                         4    31
  DEL PEAK  6(2Q37.3) WILD-TYPE     3                         4    46
D27V4, multiclass
                           clus
vv                          DEL PEAK  6(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              31
                           clus
vv                          DEL PEAK  6(2Q37.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK  7(3P21.31) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  7(3P21.31) MUTATED   14  7
  DEL PEAK  7(3P21.31) WILD-TYPE 64 29
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                            21                             93 
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                             7                             29 
$`DEL PEAK  7(3P21.31) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A3LS TCGA-DX-A3LY 
       27.19        12.85        18.54        42.44         9.04        17.10 
TCGA-DX-A3M1 TCGA-DX-A48N TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ 
       20.05        12.26         0.07         4.57         0.10         3.22 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
        7.13       143.41         5.92        22.62         6.28         1.05 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        0.10         4.08        37.55 

$`DEL PEAK  7(3P21.31) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        24.49        46.68        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        53.26        43.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       41.33         9.80        80.48        21.37         8.94         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
       73.28         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-PC-A5DK 
        2.37         0.49         5.69         4.47        11.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE 
                          9.04                          18.18 
[1] "0.1 - 143.4 (9.0)"  "0.1 - 116.9 (18.2)"
[1] "hr=" "1.6"
D28V2, continuous
D28V3, binary
                                cls
clus                              0  1
  DEL PEAK  7(3P21.31) MUTATED   13  8
  DEL PEAK  7(3P21.31) WILD-TYPE 49 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3P21.31) MUTATED     13    8
  DEL PEAK  7(3P21.31) WILD-TYPE   49   44
        clus
vv       DEL PEAK  7(3P21.31) MUTATED DEL PEAK  7(3P21.31) WILD-TYPE
  FEMALE                           13                             49
  MALE                              8                             44
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P21.31) MUTATED       2                         3    11
  DEL PEAK  7(3P21.31) WILD-TYPE     2                         5    66
D28V4, multiclass
                           clus
vv                          DEL PEAK  7(3P21.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               11
                           clus
vv                          DEL PEAK  7(3P21.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  8(3Q29) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  8(3Q29) MUTATED   16 10
  DEL PEAK  8(3Q29) WILD-TYPE 62 26
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         26                          88 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         10                          26 
$`DEL PEAK  8(3Q29) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
        2.04        27.19        12.85        18.54        46.68        74.66 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L 
       23.08        17.10        20.05        10.68        64.18        24.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-FX-A2QS TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A3OV 
       27.22        26.47         0.46         4.57         4.14        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-MJ-A68H TCGA-PC-A5DL 
        3.22         7.13        37.12        13.58         4.47        37.55 
TCGA-PC-A5DM TCGA-X6-A7WC 
        6.35        27.16 

$`DEL PEAK  8(3Q29) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        24.49        42.44        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       39.35        28.80        34.88         9.73        19.30        12.26 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ 
       16.31         2.07         7.36         1.68        16.18         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07        26.89        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       41.33         9.80        21.37         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       31.76        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         5.69        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        0.10         4.08        75.52        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.84        46.82        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       13.22         0.72        18.08         8.52 

  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                       0.46                        0.07 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                      80.48                      143.41 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                     19.295                      17.030 
[1] "0.5 - 80.5 (19.3)"  "0.1 - 143.4 (17.0)"
[1] "hr=" "1.4"
D29V2, continuous
D29V3, binary
                             cls
clus                           0  1
  DEL PEAK  8(3Q29) MUTATED   13 13
  DEL PEAK  8(3Q29) WILD-TYPE 49 39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     13   13
  DEL PEAK  8(3Q29) WILD-TYPE   49   39
        clus
vv       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  FEMALE                        13                          49
  MALE                          13                          39
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q29) MUTATED       0                         1    19
  DEL PEAK  8(3Q29) WILD-TYPE     4                         7    58
D29V4, multiclass
                           clus
vv                          DEL PEAK  8(3Q29) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            19
                           clus
vv                          DEL PEAK  8(3Q29) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              58
[1] 3 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  9(4Q35.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q35.1) MUTATED   24 14
  DEL PEAK  9(4Q35.1) WILD-TYPE 54 22
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           38                            76 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           14                            22 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ 
       27.19        12.85        46.68        74.66         6.28         8.58 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U8 TCGA-DX-A3U9 
        9.04        23.08       108.13        20.05         4.54        14.99 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-FX-A2QS 
       28.80        34.88        24.26        26.47        54.87         0.46 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       26.89         4.14         0.10        21.37         3.22         1.38 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22        13.58         5.92        22.62         6.28         1.05 
TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-UE-A6QU 
       11.70         0.10         6.35        18.08        46.82         0.72 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        24.49        18.54        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49        17.10        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UF 
       17.75        42.77        10.68        44.45        39.35        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
        9.73        19.30        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV 
        1.68        16.18         0.10         0.07         0.07         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       12.62        23.97        41.33         9.80        80.48         8.94 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        7.13        37.12        31.76        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
       73.28         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       37.55        38.63        81.01         1.84        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       21.01         3.88        13.22        18.08 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       108.13                        143.41 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       14.285                        18.080 
[1] "0.1 - 108.1 (14.3)" "0.1 - 143.4 (18.1)"
[1] "hr=" "1.7"
D30V2, continuous
D30V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   22 16
  DEL PEAK  9(4Q35.1) WILD-TYPE 40 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     22   16
  DEL PEAK  9(4Q35.1) WILD-TYPE   40   36
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          22                            40
  MALE                            16                            36
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED       3                         3    24
  DEL PEAK  9(4Q35.1) WILD-TYPE     1                         5    53
D30V4, multiclass
                           clus
vv                          DEL PEAK  9(4Q35.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              24
                           clus
vv                          DEL PEAK  9(4Q35.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                53
[1] 3 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 10(6P25.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(6P25.1) MUTATED   27 13
  DEL PEAK 10(6P25.1) WILD-TYPE 51 23
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                           40                            74 
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                           13                            23 
$`DEL PEAK 10(6P25.1) MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 
       24.49        74.66         6.28        23.08        17.10        20.05 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       10.68        39.35        28.80        34.88        64.18        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BA 
       24.26        27.22        14.96        72.72        25.08        54.87 
TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z 
       10.78         2.07        16.18         0.07         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A3RQ TCGA-IS-A3K6 
       12.62        23.97        80.48         8.94        37.12        28.21 
TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5Y9 
      143.41        22.62         1.05        71.70        36.39         2.37 
TCGA-MB-A8JL TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5VD 
        5.69        37.55        18.08        21.01 

$`DEL PEAK 10(6P25.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        9.04        70.49       108.13        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R 
        4.54        14.99        44.45         9.73        12.26        26.47 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ 
       11.47        16.31         7.36         1.68         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        0.07        26.89         0.10        41.33         9.80        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K8 
        3.22         1.38         7.13        25.22        31.76       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-KF-A41W 
       13.58        73.28         5.92         6.28         3.91        11.70 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        5.26         0.49         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52         6.35        38.63        81.01         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.08        18.18         3.88        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE 
                        22.85                         13.81 
[1] "0.1 - 143.4 (22.9)" "0.1 - 116.9 (13.8)"
[1] "hr=" "1.1"
D31V2, continuous
D31V3, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P25.1) MUTATED   24 16
  DEL PEAK 10(6P25.1) WILD-TYPE 38 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.1) MUTATED     24   16
  DEL PEAK 10(6P25.1) WILD-TYPE   38   36
        clus
vv       DEL PEAK 10(6P25.1) MUTATED DEL PEAK 10(6P25.1) WILD-TYPE
  FEMALE                          24                            38
  MALE                            16                            36
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.1) MUTATED       1                         1    34
  DEL PEAK 10(6P25.1) WILD-TYPE     3                         7    43
D31V4, multiclass
                           clus
vv                          DEL PEAK 10(6P25.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              34
                           clus
vv                          DEL PEAK 10(6P25.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                43
[1] 3 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 11(6Q14.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(6Q14.1) MUTATED   15 11
  DEL PEAK 11(6Q14.1) WILD-TYPE 63 25
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                           26                            88 
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                           11                            25 
$`DEL PEAK 11(6Q14.1) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       12.85        24.49        17.10        42.77        14.99        10.68 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A6BA TCGA-FX-A2QS 
       64.18        19.30        24.26        14.96        54.87         0.46 
TCGA-HB-A43Z TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-JV-A5VE 
        4.14        80.48         3.22        37.12        25.22         6.28 
TCGA-JV-A5VF TCGA-MB-A8JL TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.05         5.69         6.35        18.18        21.01         3.88 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

$`DEL PEAK 11(6Q14.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        27.19        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       43.04         9.04        23.08        70.49       108.13        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       15.06        17.75         4.54        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       34.88         9.73        12.26        27.22        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        1.68        16.18         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37         8.94         1.38         7.13        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
        3.91        71.70        36.39        11.70         5.26         2.37 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         4.47        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WD 
       18.08        13.22         0.72         8.52 

  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                        80.48                        143.41 
  DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE 
                       17.590                        17.915 
[1] "0.5 - 80.5 (17.6)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "1.8"
D32V2, continuous
D32V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q14.1) MUTATED   15 11
  DEL PEAK 11(6Q14.1) WILD-TYPE 47 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q14.1) MUTATED     15   11
  DEL PEAK 11(6Q14.1) WILD-TYPE   47   41
        clus
vv       DEL PEAK 11(6Q14.1) MUTATED DEL PEAK 11(6Q14.1) WILD-TYPE
  FEMALE                          15                            47
  MALE                            11                            41
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q14.1) MUTATED       0                         2    22
  DEL PEAK 11(6Q14.1) WILD-TYPE     4                         6    55
D32V4, multiclass
                           clus
vv                          DEL PEAK 11(6Q14.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              22
                           clus
vv                          DEL PEAK 11(6Q14.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK 12(6Q16.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(6Q16.1) MUTATED   13 10
  DEL PEAK 12(6Q16.1) WILD-TYPE 65 26
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                           23                            91 
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                           10                            26 
$`DEL PEAK 12(6Q16.1) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L 
       12.85        24.49        42.77        10.68        64.18        24.26 
TCGA-DX-A48P TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 
       14.96        11.47        54.87         4.57         4.14         0.10 
TCGA-IE-A3OV TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-JV-A5VE TCGA-MB-A8JL TCGA-PC-A5DO 
       80.48        37.12        25.22         6.28         5.69        81.01 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC 
       18.18        21.01         3.88        18.08        27.16 

$`DEL PEAK 12(6Q16.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        27.19        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       20.05        15.06        17.75         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       39.35        28.80        34.88         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BB TCGA-DX-A6BE 
       27.22        26.47        72.72        25.08        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07         0.07        26.89        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08         1.84        46.82        18.08        13.22         0.72 
TCGA-X6-A7WD 
        8.52 

  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                        81.01                        143.41 
  DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE 
                        18.18                         17.10 
[1] "0.1 - 81.0 (18.2)"  "0.1 - 143.4 (17.1)"
[1] "hr=" "1.4"
D33V2, continuous
D33V3, binary
                               cls
clus                             0  1
  DEL PEAK 12(6Q16.1) MUTATED   15  8
  DEL PEAK 12(6Q16.1) WILD-TYPE 47 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q16.1) MUTATED     15    8
  DEL PEAK 12(6Q16.1) WILD-TYPE   47   44
        clus
vv       DEL PEAK 12(6Q16.1) MUTATED DEL PEAK 12(6Q16.1) WILD-TYPE
  FEMALE                          15                            47
  MALE                             8                            44
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q16.1) MUTATED       0                         2    18
  DEL PEAK 12(6Q16.1) WILD-TYPE     4                         6    59
D33V4, multiclass
                           clus
vv                          DEL PEAK 12(6Q16.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              18
                           clus
vv                          DEL PEAK 12(6Q16.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  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(34) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(7Q36.3) MUTATED   16  9
  DEL PEAK 13(7Q36.3) WILD-TYPE 62 27
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           25                            89 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                            9                            27 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY 
       27.19        18.54        29.85        74.66         6.28        17.10 
TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R 
       42.77        28.80         9.73        12.26        14.96        26.47 
TCGA-DX-A6BF TCGA-DX-A6BH TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5NA TCGA-IF-A3RQ 
        2.07         1.68         4.57         4.14         9.80        37.12 
TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A5VC 
       25.22         5.92        22.62        18.08        18.08        18.18 
TCGA-UE-A6QU 
        0.72 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        12.85        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       31.56         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       70.49       108.13        20.05        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        10.68        44.45        39.35        34.88        64.18 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       19.30        24.26        27.22        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-FX-A2QS 
       54.87        10.78        16.31         7.36        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07         0.07        26.89        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD 
        6.35        38.63        81.01         1.84        46.82        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22        18.08        27.16         8.52 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.72                          0.07 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                        74.66                        143.41 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                        18.08                         17.75 
[1] "0.7 - 74.7 (18.1)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "1.6"
D34V2, continuous
D34V3, binary
                               cls
clus                             0  1
  DEL PEAK 13(7Q36.3) MUTATED   13 12
  DEL PEAK 13(7Q36.3) WILD-TYPE 49 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     13   12
  DEL PEAK 13(7Q36.3) WILD-TYPE   49   40
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          13                            49
  MALE                            12                            40
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       2                         1    16
  DEL PEAK 13(7Q36.3) WILD-TYPE     2                         7    61
D34V4, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              16
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(8P23.3) MUTATED   23 11
  DEL PEAK 14(8P23.3) WILD-TYPE 55 25
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           34                            80 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           11                            25 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3LS 
        2.04        27.19        24.49        18.54         6.28         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA 
       23.08       108.13        20.05        15.06        42.77        10.68 
TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6BK 
       44.45        28.80         9.73        19.30        26.47        16.18 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.46         0.07         4.57         4.14         0.10        41.33 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A75J TCGA-MB-A8JL 
        7.13        37.12       143.41         6.28         3.91         5.69 
TCGA-PC-A5DM TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WC 
        6.35         3.88         0.72        27.16 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        46.68        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY 
        8.58         9.70        53.26        43.04        70.49        17.10 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       17.75         4.54        14.99        39.35        34.88        64.18 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 
        1.68         0.10         0.07        26.89        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        31.76        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
        5.92        22.62         1.05        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        5.26         2.37         0.49         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52        37.55        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT 
        1.84        46.82        18.08        18.18        21.01        13.22 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        12.87                         18.08 
[1] "0.1 - 143.4 (12.9)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   17 17
  DEL PEAK 14(8P23.3) WILD-TYPE 45 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     17   17
  DEL PEAK 14(8P23.3) WILD-TYPE   45   35
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          17                            45
  MALE                            17                            35
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED       1                         2    24
  DEL PEAK 14(8P23.3) WILD-TYPE     3                         6    53
D35V4, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              24
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                53
[1] 3 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 15(9P23) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 15(9P23) MUTATED   25 12
  DEL PEAK 15(9P23) WILD-TYPE 53 24
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         37                          77 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         12                          24 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23V TCGA-DX-A23Z 
       14.04        12.85        24.49        46.68        66.87        27.81 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 
        9.04        23.08       108.13        17.10        20.05        42.77 
TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA 
       10.68        64.18         9.73        26.47        25.08        54.87 
TCGA-DX-A6BF TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ 
        2.07         0.07        26.89         0.10         8.94         3.22 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-KF-A41W TCGA-MB-A5Y9 
      143.41         5.92        22.62         3.91        11.70         2.37 
TCGA-MB-A8JL TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-QQ-A5VC 
        5.69         4.08        38.63        81.01        18.08        18.18 
TCGA-X6-A7WC 
       27.16 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.54        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ 
       74.66         5.26        76.41         6.28        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.70        53.26        43.04        70.49        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        44.45        39.35        28.80        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.46         0.10         0.07         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97        41.33         9.80        80.48        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        7.13        37.12        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28         6.28         1.05        71.70        36.39 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        5.26         0.49         4.47        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD 
       37.55         6.35        18.08         1.84        46.82        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
        3.88        13.22         0.72        18.08         8.52 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     143.41                      116.88 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                      18.18                       16.31 
[1] "0.1 - 143.4 (18.2)" "0.1 - 116.9 (16.3)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                             cls
clus                           0  1
  DEL PEAK 15(9P23) MUTATED   22 15
  DEL PEAK 15(9P23) WILD-TYPE 40 37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     22   15
  DEL PEAK 15(9P23) WILD-TYPE   40   37
        clus
vv       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  FEMALE                        22                          40
  MALE                          15                          37
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED       1                         3    27
  DEL PEAK 15(9P23) WILD-TYPE     3                         5    50
D36V4, multiclass
                           clus
vv                          DEL PEAK 15(9P23) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            27
                           clus
vv                          DEL PEAK 15(9P23) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              50
[1] 3 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 16(9P21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(9P21.3) MUTATED   33 14
  DEL PEAK 16(9P21.3) WILD-TYPE 45 22
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           47                            67 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           14                            22 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW 
       42.44        74.66        66.87         6.28         9.04       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       17.10        20.05        15.06        42.77         4.54        10.68 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA 
       28.80        64.18         9.73        26.47        25.08        54.87 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        2.07        16.18         0.46         0.07         0.07        26.89 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 
        0.10         8.94         3.22       143.41         5.92        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN 
       11.70         2.37         5.69         0.10         4.08        38.63 
TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU TCGA-X6-A7WC 
       81.01        18.08        18.18         0.72        27.16 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
        2.04        31.56        29.85         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        53.26        43.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       70.49        17.75        14.99        44.45        39.35        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ 
       11.47        10.78        16.31         7.36         1.68         0.10 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       31.76        28.21       116.88        13.58        73.28         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA 
        1.05         3.91        71.70        36.39         5.26         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP 
        4.47        11.08        75.52        37.55         6.35        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
        1.84        46.82        21.01         3.88        13.22        18.08 
TCGA-X6-A7WD 
        8.52 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                        17.10                         18.08 
[1] "0.1 - 143.4 (17.1)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.1"
D37V2, continuous
D37V3, binary
                               cls
clus                             0  1
  DEL PEAK 16(9P21.3) MUTATED   28 19
  DEL PEAK 16(9P21.3) WILD-TYPE 34 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     28   19
  DEL PEAK 16(9P21.3) WILD-TYPE   34   33
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          28                            34
  MALE                            19                            33
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED       3                         3    30
  DEL PEAK 16(9P21.3) WILD-TYPE     1                         5    47
D37V4, multiclass
                           clus
vv                          DEL PEAK 16(9P21.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              30
                           clus
vv                          DEL PEAK 16(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                47
[1] 3 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 17(9Q34.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 17(9Q34.3) MUTATED   15 12
  DEL PEAK 17(9Q34.3) WILD-TYPE 63 24
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           27                            87 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           12                            24 
$`DEL PEAK 17(9Q34.3) MUTATED`
TCGA-DX-A1KU TCGA-DX-A3M1 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48R 
       14.04        20.05        39.35        28.80         9.73        26.47 
TCGA-DX-A48V TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       25.08         0.07        26.89         4.57        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 
        9.80        80.48        21.37        25.22        13.58         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R 
        6.28         1.05         3.91         5.69         4.47         0.10 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-X6-A7WB 
        6.35        81.01        18.08 

$`DEL PEAK 17(9Q34.3) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       10.68        44.45        34.88        64.18        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA 
       12.26        27.22        14.96        72.72        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
        0.46         0.10         0.07         4.14        12.62        41.33 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        8.94         3.22         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PN 
       28.21       143.41       116.88        73.28        22.62        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J 
       36.39        11.70         5.26         2.37         0.49        11.08 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.08        75.52        37.55        38.63        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       46.82        18.08        18.18        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        27.16         8.52 

  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                        81.01                        143.41 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                        13.58                         18.08 
[1] "0.1 - 81.0 (13.6)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.1"
D38V2, continuous
D38V3, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.3) MUTATED   17 10
  DEL PEAK 17(9Q34.3) WILD-TYPE 45 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED     17   10
  DEL PEAK 17(9Q34.3) WILD-TYPE   45   42
        clus
vv       DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                          17                            45
  MALE                            10                            42
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9Q34.3) MUTATED       1                         5    18
  DEL PEAK 17(9Q34.3) WILD-TYPE     3                         3    59
D38V4, multiclass
                           clus
vv                          DEL PEAK 17(9Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              18
                           clus
vv                          DEL PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                 3
  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(39) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10P15.3) MUTATED   42 16
  DEL PEAK 18(10P15.3) WILD-TYPE 36 20
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            58                             56 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            16                             20 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
        2.04        27.19        18.54        42.44        74.66         6.28 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UE 
      108.13        17.10        15.06        10.68        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B9 
       64.18        19.30        12.26        14.96        26.47        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT 
       54.87        10.78        16.18         0.46         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
        4.57         4.14        12.62        23.97         0.10        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 
        8.94         3.22         7.13        25.22        31.76       143.41 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-KF-A41W 
        5.92        22.62         6.28         3.91        71.70        11.70 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       37.55         6.35        81.01        46.82        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88         0.72        27.16         8.52 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        24.49        46.68        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       20.05        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V 
       39.35         9.73        24.26        27.22        72.72        25.08 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ TCGA-FX-A48G 
       16.31         2.07         7.36         1.68         0.10         0.07 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
       41.33         9.80        21.37         1.38        37.12        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-LI-A67I 
      116.88        13.58        73.28         1.05        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        2.37        11.08        38.63        18.08         1.84        18.08 
TCGA-UE-A6QT TCGA-X6-A7WB 
       13.22        18.08 

  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        15.010                         19.065 
[1] "0.1 - 143.4 (15.0)" "0.1 - 116.9 (19.1)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   36 22
  DEL PEAK 18(10P15.3) WILD-TYPE 26 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     36   22
  DEL PEAK 18(10P15.3) WILD-TYPE   26   30
        clus
vv       DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  FEMALE                           36                             26
  MALE                             22                             30
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P15.3) MUTATED       3                         5    42
  DEL PEAK 18(10P15.3) WILD-TYPE     1                         3    35
D39V4, multiclass
                           clus
vv                          DEL PEAK 18(10P15.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               42
                           clus
vv                          DEL PEAK 18(10P15.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D40V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 19(10Q23.31) MUTATED   42 22
  DEL PEAK 19(10Q23.31) WILD-TYPE 36 14
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             64                              50 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             22                              14 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 
       27.19        24.49        18.54         6.28        42.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A3NJ 
       11.47        54.87        10.78         2.07        16.18         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97         0.10        41.33        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38         7.13        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      143.41        13.58        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
       71.70        11.70         0.49         4.47         0.10         4.08 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VC 
       37.55         6.35        81.01        18.08        46.82        18.18 
TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01        18.08        27.16         8.52 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE 
       17.75         4.54        44.45        12.26        25.08        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IS-A3K8 
        7.36         1.68         0.46         9.80        37.12       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL 
       73.28         5.92        36.39         5.26         2.37         5.69 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-SG-A6Z7 
       11.08        75.52        38.63         1.84        18.08         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU 
       13.22         0.72 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           0.07                            0.46 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         143.41                          116.88 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         18.080                          17.425 
[1] "0.1 - 143.4 (18.1)" "0.5 - 116.9 (17.4)"
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                                 cls
clus                               0  1
  DEL PEAK 19(10Q23.31) MUTATED   42 22
  DEL PEAK 19(10Q23.31) WILD-TYPE 20 30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     42   22
  DEL PEAK 19(10Q23.31) WILD-TYPE   20   30
        clus
vv       DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  FEMALE                            42                              20
  MALE                              22                              30
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.31) MUTATED       2                         7    48
  DEL PEAK 19(10Q23.31) WILD-TYPE     2                         1    29
D40V4, multiclass
                           clus
vv                          DEL PEAK 19(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                48
                           clus
vv                          DEL PEAK 19(10Q23.31) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 20(11P15.5) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(11P15.5) MUTATED   30 17
  DEL PEAK 20(11P15.5) WILD-TYPE 48 19
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            47                             67 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            17                             19 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y 
       14.04         2.04        27.19        24.49        42.44         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.70         9.04        23.08       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       15.06        42.77        14.99        28.80        34.88        64.18 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-FX-A3RE TCGA-FX-A48G 
       24.26        12.26        27.22        14.96         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M5 
       41.33         8.94         7.13        25.22        31.76         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO 
       22.62         1.05        71.70        37.55         6.35        81.01 
TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       18.18         3.88         0.72        18.08        27.16 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       12.85        18.54        46.68        31.56        29.85        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA 
       53.26        43.04        70.49        17.75         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A48U 
       44.45        39.35         9.73        19.30        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HS-A5NA 
        7.36         1.68        16.18         0.46         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
       80.48        21.37         3.22         1.38        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
      143.41       116.88        13.58        73.28         6.28         3.91 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN 
        4.47        11.08         0.10         4.08        75.52        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT 
       18.08         1.84        46.82        18.08        21.01        13.22 
TCGA-X6-A7WD 
        8.52 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          0.07                           0.10 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        108.13                         143.41 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                         18.08                          17.75 
[1] "0.1 - 108.1 (18.1)" "0.1 - 143.4 (17.8)"
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
                                cls
clus                              0  1
  DEL PEAK 20(11P15.5) MUTATED   27 20
  DEL PEAK 20(11P15.5) WILD-TYPE 35 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     27   20
  DEL PEAK 20(11P15.5) WILD-TYPE   35   32
        clus
vv       DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  FEMALE                           27                             35
  MALE                             20                             32
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.5) MUTATED       2                         2    34
  DEL PEAK 20(11P15.5) WILD-TYPE     2                         6    43
D41V4, multiclass
                           clus
vv                          DEL PEAK 20(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               34
                           clus
vv                          DEL PEAK 20(11P15.5) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 43
[1] 3 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 21(11Q24.3) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11Q24.3) MUTATED   29 17
  DEL PEAK 21(11Q24.3) WILD-TYPE 49 19
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                            46                             68 
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                            17                             19 
$`DEL PEAK 21(11Q24.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
        2.04        27.19        12.85        24.49        18.54        42.44 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LY 
       74.66         5.26         6.28         9.70        53.26        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48K 
       20.05        15.06        42.77        14.99        28.80        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA TCGA-DX-A6BF 
       12.26        27.22        26.47        72.72        54.87         2.07 
TCGA-DX-A6BK TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A3OV 
       16.18        26.89         4.57        12.62        41.33        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 
        3.22         7.13        37.12        31.76        13.58         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MO-A47R 
       22.62         1.05        11.70         5.26         2.37         0.10 
TCGA-PC-A5DM TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-X6-A7WC 
        6.35        18.08         3.88        27.16 

$`DEL PEAK 21(11Q24.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23V 
       14.04        46.68        31.56        29.85        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81        60.30         8.58        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       70.49       108.13        17.75         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P 
       39.35        34.88        64.18         9.73        24.26        14.96 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       25.08        11.47        10.78        16.31         7.36         1.68 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N7 
        0.46         0.10         0.07         0.07         4.14        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
        0.10         9.80        21.37         8.94         1.38        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
       28.21       143.41       116.88        73.28         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       71.70        36.39         0.49         5.69         4.47        11.08 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52        37.55        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
        1.84        46.82        18.18        21.01        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                         80.48                         143.41 
  DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE 
                         16.64                          18.08 
[1] "0.1 - 80.5 (16.6)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.7"
D42V2, continuous
D42V3, binary
                                cls
clus                              0  1
  DEL PEAK 21(11Q24.3) MUTATED   23 23
  DEL PEAK 21(11Q24.3) WILD-TYPE 39 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q24.3) MUTATED     23   23
  DEL PEAK 21(11Q24.3) WILD-TYPE   39   29
        clus
vv       DEL PEAK 21(11Q24.3) MUTATED DEL PEAK 21(11Q24.3) WILD-TYPE
  FEMALE                           23                             39
  MALE                             23                             29
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11Q24.3) MUTATED       2                         2    30
  DEL PEAK 21(11Q24.3) WILD-TYPE     2                         6    47
D42V4, multiclass
                           clus
vv                          DEL PEAK 21(11Q24.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               30
                           clus
vv                          DEL PEAK 21(11Q24.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 47
[1] 3 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 22(12P13.1) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(12P13.1) MUTATED   22 11
  DEL PEAK 22(12P13.1) WILD-TYPE 56 25
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                            33                             81 
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                            11                             25 
$`DEL PEAK 22(12P13.1) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
        2.04        27.19        18.54        46.68        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 
        9.70        23.08       108.13        17.10        15.06        42.77 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BK TCGA-FX-A3NJ 
       14.99        28.80        12.26        25.08        16.18         0.10 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IS-A3K6 TCGA-JV-A5VF TCGA-KF-A41W 
       23.97        41.33         7.13        28.21         1.05        11.70 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
        4.47         6.35        81.01        46.82        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WD 
        3.88         0.72         8.52 

$`DEL PEAK 22(12P13.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        24.49        42.44        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U6 
       53.26        43.04         9.04        70.49        20.05        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
        4.54        10.68        44.45        39.35        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        7.36         1.68         0.46         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.57         4.14        12.62         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37         8.94         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       31.76       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
       22.62         6.28         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         5.69        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       75.52        37.55        38.63        18.08         1.84        18.08 
TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
       13.22        18.08        27.16 

  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                        108.13                         143.41 
  DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE 
                         17.10                          18.08 
[1] "0.1 - 108.1 (17.1)" "0.1 - 143.4 (18.1)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                                cls
clus                              0  1
  DEL PEAK 22(12P13.1) MUTATED   15 18
  DEL PEAK 22(12P13.1) WILD-TYPE 47 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12P13.1) MUTATED     15   18
  DEL PEAK 22(12P13.1) WILD-TYPE   47   34
        clus
vv       DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE
  FEMALE                           15                             47
  MALE                             18                             34
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(12P13.1) MUTATED       1                         2    21
  DEL PEAK 22(12P13.1) WILD-TYPE     3                         6    56
D43V4, multiclass
                           clus
vv                          DEL PEAK 22(12P13.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               21
                           clus
vv                          DEL PEAK 22(12P13.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 23(12Q12) MUTATION ANALYSIS
D44V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 23(12Q12) MUTATED   15  7
  DEL PEAK 23(12Q12) WILD-TYPE 63 29
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                          22                           92 
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                           7                           29 
$`DEL PEAK 23(12Q12) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 
        2.04        46.68        74.66         6.28         8.58         9.70 
TCGA-DX-A3LY TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6BF TCGA-FX-A3NJ 
       17.10        39.35        64.18        26.47         2.07         0.10 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-JV-A5VF TCGA-KF-A41W 
       12.62        23.97        21.37        25.22         1.05        11.70 
TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-X6-A7WD 
        4.47        81.01        46.82         8.52 

$`DEL PEAK 23(12Q12) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        27.19        12.85        24.49        18.54        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
       60.30        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      108.13        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       14.99        10.68        44.45        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       25.08        11.47        54.87        10.78        16.31         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        1.68        16.18         0.46         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.57         4.14         0.10        41.33         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        8.94         3.22         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
       22.62         6.28         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         5.69        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55         6.35        38.63        18.08         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                       81.01                       143.41 
  DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE 
                       14.86                        18.08 
[1] "0.1 - 81.0 (14.9)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
                              cls
clus                            0  1
  DEL PEAK 23(12Q12) MUTATED   12 10
  DEL PEAK 23(12Q12) WILD-TYPE 50 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(12Q12) MUTATED     12   10
  DEL PEAK 23(12Q12) WILD-TYPE   50   42
        clus
vv       DEL PEAK 23(12Q12) MUTATED DEL PEAK 23(12Q12) WILD-TYPE
  FEMALE                         12                           50
  MALE                           10                           42
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(12Q12) MUTATED       0                         2    13
  DEL PEAK 23(12Q12) WILD-TYPE     4                         6    64
D44V4, multiclass
                           clus
vv                          DEL PEAK 23(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             13
                           clus
vv                          DEL PEAK 23(12Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 24(13Q14.2) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(13Q14.2) MUTATED   51 28
  DEL PEAK 24(13Q14.2) WILD-TYPE 27  8
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                            79                             35 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                            28                              8 
$`DEL PEAK 24(13Q14.2) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY 
       74.66         6.28         9.70         9.04        23.08        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       20.05        42.77        14.99        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF 
       26.47        72.72        25.08        54.87        10.78         2.07 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        7.13        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MO-A47R 
       71.70        11.70         2.37         0.49         5.69         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52        37.55         6.35        81.01        18.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC 
       46.82        18.08        18.18         3.88        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

$`DEL PEAK 24(13Q14.2) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
        2.04        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81        60.30         8.58        53.26        43.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA 
       70.49       108.13        15.06        17.75         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       44.45        12.26        11.47        16.31         7.36         1.68 
TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-LI-A67I TCGA-MJ-A68H TCGA-MJ-A68J 
      116.88         5.92        36.39         5.26         4.47        11.08 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       38.63         1.84        21.01        13.22         0.72 

  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                          0.07                           0.72 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE 
                         18.08                          16.31 
[1] "0.1 - 143.4 (18.1)" "0.7 - 116.9 (16.3)"
[1] "hr=" "1.8"
D45V2, continuous
D45V3, binary
                                cls
clus                              0  1
  DEL PEAK 24(13Q14.2) MUTATED   48 31
  DEL PEAK 24(13Q14.2) WILD-TYPE 14 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(13Q14.2) MUTATED     48   31
  DEL PEAK 24(13Q14.2) WILD-TYPE   14   21
        clus
vv       DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE
  FEMALE                           48                             14
  MALE                             31                             21
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(13Q14.2) MUTATED       2                         5    60
  DEL PEAK 24(13Q14.2) WILD-TYPE     2                         3    17
D45V4, multiclass
                           clus
vv                          DEL PEAK 24(13Q14.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               60
                           clus
vv                          DEL PEAK 24(13Q14.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 25(14Q24.1) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(14Q24.1) MUTATED   29  8
  DEL PEAK 25(14Q24.1) WILD-TYPE 49 28
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                            37                             77 
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                             8                             28 
$`DEL PEAK 25(14Q24.1) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       42.44        74.66        23.08        70.49        17.10        15.06 
TCGA-DX-A3UE TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-FX-A2QS 
       34.88        12.26        27.22        14.96        72.72         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5NA 
        0.10         0.07         0.07         4.14         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       21.37         3.22        28.21       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-QQ-A5V9 TCGA-X6-A7WB 
       22.62         6.28         1.05        11.70        46.82        18.08 
TCGA-X6-A7WC 
       27.16 

$`DEL PEAK 25(14Q24.1) WILD-TYPE`
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       46.68        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 
       43.04         9.04       108.13        20.05        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V 
       64.18         9.73        19.30        24.26        26.47        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        1.68        16.18        26.89         4.57        12.62        23.97 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       41.33        80.48         8.94         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN 
       25.22        31.76        13.58         5.92         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39         5.26         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        81.01        18.08         1.84        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WD 
       21.01         3.88        13.22         0.72         8.52 

  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                          0.07                           0.10 
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                        143.41                         108.13 
  DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE 
                         18.08                          17.75 
[1] "0.1 - 143.4 (18.1)" "0.1 - 108.1 (17.8)"
[1] "hr=" "1.8"
D46V2, continuous
D46V3, binary
                                cls
clus                              0  1
  DEL PEAK 25(14Q24.1) MUTATED   22 15
  DEL PEAK 25(14Q24.1) WILD-TYPE 40 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(14Q24.1) MUTATED     22   15
  DEL PEAK 25(14Q24.1) WILD-TYPE   40   37
        clus
vv       DEL PEAK 25(14Q24.1) MUTATED DEL PEAK 25(14Q24.1) WILD-TYPE
  FEMALE                           22                             40
  MALE                             15                             37
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(14Q24.1) MUTATED       1                         2    25
  DEL PEAK 25(14Q24.1) WILD-TYPE     3                         6    52
D46V4, multiclass
                           clus
vv                          DEL PEAK 25(14Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               25
                           clus
vv                          DEL PEAK 25(14Q24.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 26(15Q11.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(15Q11.2) MUTATED   12  7
  DEL PEAK 26(15Q11.2) WILD-TYPE 66 29
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                            19                             95 
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                             7                             29 
$`DEL PEAK 26(15Q11.2) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3UA TCGA-DX-A3UB 
       14.04         2.04         9.04        23.08        10.68        44.45 
TCGA-DX-A48O TCGA-DX-A6BF TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ 
       27.22         2.07         0.46        26.89         3.22         7.13 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-PC-A5DM 
       37.12       143.41        73.28         5.92         6.28         6.35 
TCGA-QQ-A5VA 
       18.08 

$`DEL PEAK 26(15Q11.2) WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       43.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75        42.77         4.54        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ 
       10.78        16.31         7.36         1.68        16.18         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         1.05         3.91        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
       18.08         1.84        46.82        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE 
                         10.68                          18.08 
[1] "0.5 - 143.4 (10.7)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.4"
D47V2, continuous
D47V3, binary
                                cls
clus                              0  1
  DEL PEAK 26(15Q11.2) MUTATED   14  5
  DEL PEAK 26(15Q11.2) WILD-TYPE 48 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q11.2) MUTATED     14    5
  DEL PEAK 26(15Q11.2) WILD-TYPE   48   47
        clus
vv       DEL PEAK 26(15Q11.2) MUTATED DEL PEAK 26(15Q11.2) WILD-TYPE
  FEMALE                           14                             48
  MALE                              5                             47
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(15Q11.2) MUTATED       0                         2    16
  DEL PEAK 26(15Q11.2) WILD-TYPE     4                         6    61
D47V4, multiclass
                           clus
vv                          DEL PEAK 26(15Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               16
                           clus
vv                          DEL PEAK 26(15Q11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 27(16Q12.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 27(16Q12.1) MUTATED   42 21
  DEL PEAK 27(16Q12.1) WILD-TYPE 36 15
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                            63                             51 
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                            21                             15 
$`DEL PEAK 27(16Q12.1) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       14.04        27.19        18.54        74.66         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 
       23.08        17.10        20.05        15.06        42.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       10.68        39.35        28.80        64.18        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB 
       27.22        14.96        26.47        25.08        54.87        10.78 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.10         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       12.62         0.10         9.80        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28         6.28         1.05         3.91        71.70 
TCGA-KF-A41W TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
       11.70         5.69         4.47         0.10         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
        6.35        81.01        18.08        46.82        18.18        21.01 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
        0.72        18.08         8.52 

$`DEL PEAK 27(16Q12.1) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N 
       17.75         4.54        44.45        34.88         9.73        12.26 
TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       72.72        11.47        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IS-A3K7 
       16.18         0.46        23.97        41.33        80.48       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
      116.88         5.92        22.62        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        0.49        11.08        75.52        38.63         1.84        18.08 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
        3.88        13.22        27.16 

  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                          0.07                           0.46 
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                         81.01                         143.41 
  DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE 
                         15.06                          22.62 
[1] "0.1 - 81.0 (15.1)"  "0.5 - 143.4 (22.6)"
[1] "hr=" "1.6"
D48V2, continuous
D48V3, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q12.1) MUTATED   40 23
  DEL PEAK 27(16Q12.1) WILD-TYPE 22 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q12.1) MUTATED     40   23
  DEL PEAK 27(16Q12.1) WILD-TYPE   22   29
        clus
vv       DEL PEAK 27(16Q12.1) MUTATED DEL PEAK 27(16Q12.1) WILD-TYPE
  FEMALE                           40                             22
  MALE                             23                             29
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(16Q12.1) MUTATED       2                         5    49
  DEL PEAK 27(16Q12.1) WILD-TYPE     2                         3    28
D48V4, multiclass
                           clus
vv                          DEL PEAK 27(16Q12.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               49
                           clus
vv                          DEL PEAK 27(16Q12.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 28(16Q23.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(16Q23.1) MUTATED   44 20
  DEL PEAK 28(16Q23.1) WILD-TYPE 34 16
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                            64                             50 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                            20                             16 
$`DEL PEAK 28(16Q23.1) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       14.04        18.54        42.44        74.66         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       23.08        17.10        15.06        42.77        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       39.35        28.80        64.18        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ 
       14.96        26.47        25.08        54.87        10.78         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       23.97         0.10         9.80        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA 
        1.38         7.13        37.12        25.22        31.76        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
       73.28         5.92        22.62         6.28         1.05        71.70 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
       11.70         2.37         5.69         4.47         0.10         4.08 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VC 
       37.55         6.35        81.01        18.08        46.82        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01         0.72        18.08         8.52 

$`DEL PEAK 28(16Q23.1) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J 
       20.05        17.75         4.54        44.45        34.88         9.73 
TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       12.26        72.72        11.47        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IS-A3K6 
        1.68        16.18         0.46        41.33        80.48        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-JV-A75J TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA 
      143.41       116.88         3.91        36.39         5.26         0.49 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-SG-A6Z7 
       11.08        75.52        38.63         1.84        18.08         3.88 
TCGA-UE-A6QT TCGA-X6-A7WC 
       13.22        27.16 

  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                          0.07                           0.46 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                         81.01                         143.41 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                        15.025                         22.270 
[1] "0.1 - 81.0 (15.0)"  "0.5 - 143.4 (22.3)"
[1] "hr=" "1.4"
D49V2, continuous
D49V3, binary
                                cls
clus                              0  1
  DEL PEAK 28(16Q23.1) MUTATED   40 24
  DEL PEAK 28(16Q23.1) WILD-TYPE 22 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q23.1) MUTATED     40   24
  DEL PEAK 28(16Q23.1) WILD-TYPE   22   28
        clus
vv       DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE
  FEMALE                           40                             22
  MALE                             24                             28
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16Q23.1) MUTATED       3                         5    48
  DEL PEAK 28(16Q23.1) WILD-TYPE     1                         3    29
D49V4, multiclass
                           clus
vv                          DEL PEAK 28(16Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               48
                           clus
vv                          DEL PEAK 28(16Q23.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 29(17P13.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(17P13.1) MUTATED   35 15
  DEL PEAK 29(17P13.1) WILD-TYPE 43 21
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                            50                             64 
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                            15                             21 
$`DEL PEAK 29(17P13.1) MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       24.49        74.66        23.08        42.77        14.99        10.68 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       16.18         0.10        26.89        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33         9.80        80.48        21.37         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE 
        7.13        31.76        28.21       143.41         5.92         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-PC-A5DK 
        3.91        71.70        11.70         5.26         0.49        75.52 
TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QU 
       37.55        18.08        18.18        21.01         3.88         0.72 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

$`DEL PEAK 29(17P13.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       15.06        17.75         4.54        44.45        39.35        28.80 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       64.18        12.26        16.31         2.07         7.36         1.68 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A4EI 
        0.46         0.07         0.07         4.57         4.14         8.94 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       37.12        25.22       116.88        13.58        73.28        22.62 
TCGA-JV-A5VF TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        1.05        36.39         2.37         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 
        0.10         4.08         6.35        38.63        81.01         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-X6-A7WC 
       46.82        18.08        13.22        27.16 

  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE 
                        18.130                         16.705 
[1] "0.1 - 143.4 (18.1)" "0.1 - 116.9 (16.7)"
[1] "hr=" "1"  
D50V2, continuous
D50V3, binary
                                cls
clus                              0  1
  DEL PEAK 29(17P13.1) MUTATED   33 17
  DEL PEAK 29(17P13.1) WILD-TYPE 29 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17P13.1) MUTATED     33   17
  DEL PEAK 29(17P13.1) WILD-TYPE   29   35
        clus
vv       DEL PEAK 29(17P13.1) MUTATED DEL PEAK 29(17P13.1) WILD-TYPE
  FEMALE                           33                             29
  MALE                             17                             35
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(17P13.1) MUTATED       1                         4    39
  DEL PEAK 29(17P13.1) WILD-TYPE     3                         4    38
D50V4, multiclass
                           clus
vv                          DEL PEAK 29(17P13.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               39
                           clus
vv                          DEL PEAK 29(17P13.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 30(17Q11.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(17Q11.2) MUTATED   17 11
  DEL PEAK 30(17Q11.2) WILD-TYPE 61 25
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                            28                             86 
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                            11                             25 
$`DEL PEAK 30(17Q11.2) MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW 
       24.49        74.66         6.28         9.70        23.08       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L 
       20.05        14.99        10.68        28.80        64.18        24.26 
TCGA-DX-A6BF TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
        2.07        26.89         4.14         3.22         7.13        25.22 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-MB-A8JL TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5V9 
        5.92         3.91         5.69         4.08         6.35        46.82 
TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WC 
       18.18         3.88         0.72        27.16 

$`DEL PEAK 30(17Q11.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        53.26        43.04         9.04 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49        17.10        15.06        17.75        42.77         4.54 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       44.45        39.35        34.88         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       54.87        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
        0.46         0.10         0.07         0.07         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        8.94         1.38        37.12        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62         6.28         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
        4.47        11.08         0.10        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT 
       81.01        18.08         1.84        18.08        21.01        13.22 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                          0.72                           0.07 
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                        108.13                         143.41 
  DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE 
                        12.835                         18.080 
[1] "0.7 - 108.1 (12.8)" "0.1 - 143.4 (18.1)"
[1] "hr=" "1.7"
D51V2, continuous
D51V3, binary
                                cls
clus                              0  1
  DEL PEAK 30(17Q11.2) MUTATED   16 12
  DEL PEAK 30(17Q11.2) WILD-TYPE 46 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17Q11.2) MUTATED     16   12
  DEL PEAK 30(17Q11.2) WILD-TYPE   46   40
        clus
vv       DEL PEAK 30(17Q11.2) MUTATED DEL PEAK 30(17Q11.2) WILD-TYPE
  FEMALE                           16                             46
  MALE                             12                             40
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(17Q11.2) MUTATED       1                         2    21
  DEL PEAK 30(17Q11.2) WILD-TYPE     3                         6    56
D51V4, multiclass
                           clus
vv                          DEL PEAK 30(17Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               21
                           clus
vv                          DEL PEAK 30(17Q11.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 31(17Q25.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(17Q25.3) MUTATED   17 12
  DEL PEAK 31(17Q25.3) WILD-TYPE 61 24
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                            29                             85 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                            12                             24 
$`DEL PEAK 31(17Q25.3) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT 
        2.04        27.19        18.54        74.66         6.28        23.08 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       17.10        20.05        14.99        28.80        34.88        64.18 
TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 
       24.26        54.87        10.78         0.10        12.62        23.97 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-JV-A5VE 
       80.48        21.37         3.22        25.22        13.58         6.28 
TCGA-KF-A41W TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-X6-A7WC 
       11.70        37.55         6.35        46.82        27.16 

$`DEL PEAK 31(17Q25.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        53.26        43.04         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
      108.13        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       44.45        39.35         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BE 
       14.96        26.47        72.72        25.08        11.47        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE 
        2.07         7.36         1.68        16.18         0.46         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07        26.89         4.57         4.14         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        9.80         8.94         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       75.52        38.63        81.01        18.08         1.84        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01         3.88        13.22         0.72        18.08 
TCGA-X6-A7WD 
        8.52 

  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                         80.48                         143.41 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                         21.37                          16.18 
[1] "0.1 - 80.5 (21.4)"  "0.1 - 143.4 (16.2)"
[1] "hr=" "1.4"
D52V2, continuous
D52V3, binary
                                cls
clus                              0  1
  DEL PEAK 31(17Q25.3) MUTATED   13 16
  DEL PEAK 31(17Q25.3) WILD-TYPE 49 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q25.3) MUTATED     13   16
  DEL PEAK 31(17Q25.3) WILD-TYPE   49   36
        clus
vv       DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE
  FEMALE                           13                             49
  MALE                             16                             36
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17Q25.3) MUTATED       0                         1    22
  DEL PEAK 31(17Q25.3) WILD-TYPE     4                         7    55
D52V4, multiclass
                           clus
vv                          DEL PEAK 31(17Q25.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               22
                           clus
vv                          DEL PEAK 31(17Q25.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 32(18Q23) MUTATION ANALYSIS
D53V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 32(18Q23) MUTATED   22 13
  DEL PEAK 32(18Q23) WILD-TYPE 56 23
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          35                           79 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          13                           23 
$`DEL PEAK 32(18Q23) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A2J0 
       27.19        12.85        46.68        31.56         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF 
       23.08        20.05        15.06        42.77        10.68        64.18 
TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A48G 
       19.30        14.96        54.87         2.07        16.18         0.07 
TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ 
       26.89        12.62        23.97        80.48         3.22        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
      143.41        22.62         1.05        11.70         5.26         2.37 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-SG-A6Z7 TCGA-UE-A6QU 
        6.35        18.08        46.82         3.88         0.72 

$`DEL PEAK 32(18Q23) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 
       14.04         2.04        24.49        18.54        42.44        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.10        17.75         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        24.26        12.26        27.22 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47        72.72        25.08        11.47        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A3YV 
        7.36         1.68         0.46         0.10         0.07         4.57 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
        4.14         0.10        41.33         9.80        21.37         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38         7.13        37.12        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28         5.92         6.28         3.91        71.70 
TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
       36.39         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 
        4.08        75.52        37.55        38.63        81.01         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        18.18        21.01        13.22        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      143.41                       116.88 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                       16.18                        18.08 
[1] "0.1 - 143.4 (16.2)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.4"
D53V2, continuous
D53V3, binary
                              cls
clus                            0  1
  DEL PEAK 32(18Q23) MUTATED   21 14
  DEL PEAK 32(18Q23) WILD-TYPE 41 38
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     21   14
  DEL PEAK 32(18Q23) WILD-TYPE   41   38
        clus
vv       DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  FEMALE                         21                           41
  MALE                           14                           38
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(18Q23) MUTATED       2                         2    24
  DEL PEAK 32(18Q23) WILD-TYPE     2                         6    53
D53V4, multiclass
                           clus
vv                          DEL PEAK 32(18Q23) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             24
                           clus
vv                          DEL PEAK 32(18Q23) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               53
[1] 3 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 33(19P13.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(19P13.3) MUTATED   24  9
  DEL PEAK 33(19P13.3) WILD-TYPE 54 27
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            33                             81 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                             9                             27 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6B9 
      108.13        42.77        39.35        64.18        26.47        11.47 
TCGA-DX-A6BA TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       54.87         0.07         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       41.33        21.37         8.94         7.13        25.22        31.76 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN 
      143.41        13.58         5.92        22.62         1.05        71.70 
TCGA-KF-A41W TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5VD 
       11.70         5.26         4.08         6.35        81.01        21.01 
TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC 
        3.88        18.08        27.16 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        28.80        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5NA 
        0.46         0.10         0.07        26.89         4.57         9.80 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K8 
       80.48         3.22         1.38        37.12        28.21       116.88 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A5YA 
       73.28         6.28         3.91        36.39         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47        11.08         0.10        75.52        37.55 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        18.08         1.84        46.82        18.08        18.18 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WD 
       13.22         0.72         8.52 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                         21.01                          17.10 
[1] "0.1 - 143.4 (21.0)" "0.1 - 116.9 (17.1)"
[1] "hr=" "1.5"
D54V2, continuous
D54V3, binary
                                cls
clus                              0  1
  DEL PEAK 33(19P13.3) MUTATED   26  7
  DEL PEAK 33(19P13.3) WILD-TYPE 36 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     26    7
  DEL PEAK 33(19P13.3) WILD-TYPE   36   45
        clus
vv       DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  FEMALE                           26                             36
  MALE                              7                             45
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.3) MUTATED       1                         3    26
  DEL PEAK 33(19P13.3) WILD-TYPE     3                         5    51
D54V4, multiclass
                           clus
vv                          DEL PEAK 33(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               26
                           clus
vv                          DEL PEAK 33(19P13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 51
[1] 3 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 34(19Q13.43) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 34(19Q13.43) MUTATED   27 14
  DEL PEAK 34(19Q13.43) WILD-TYPE 51 22
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                             41                              73 
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                             14                              22 
$`DEL PEAK 34(19Q13.43) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U7 
        2.04        12.85        74.66         9.70        23.08        42.77 
TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48U 
       10.68        28.80        24.26        12.26        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       25.08        11.47        54.87         1.68        16.18         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        0.07         0.07         4.57        12.62        23.97         9.80 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       80.48         3.22        31.76        13.58        73.28        22.62 
TCGA-K1-A3PN TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP 
       71.70         5.26         4.08        75.52        81.01        18.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WD 
       46.82        18.18         3.88        18.08         8.52 

$`DEL PEAK 34(19Q13.43) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        53.26        43.04         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
        4.54        14.99        44.45        39.35        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6BB TCGA-DX-A6BE 
        9.73        19.30        27.22        26.47        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 
        2.07         7.36         0.10        26.89         4.14         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       41.33        21.37         8.94         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22        28.21       143.41       116.88         5.92         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA 
        1.05         3.91        36.39        11.70         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM 
        5.69         4.47        11.08         0.10        37.55         6.35 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       38.63         1.84        18.08        21.01        13.22         0.72 
TCGA-X6-A7WC 
       27.16 

  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                           0.07                            0.10 
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                          81.01                          143.41 
  DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE 
                          16.18                           18.08 
[1] "0.1 - 81.0 (16.2)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                                 cls
clus                               0  1
  DEL PEAK 34(19Q13.43) MUTATED   27 14
  DEL PEAK 34(19Q13.43) WILD-TYPE 35 38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(19Q13.43) MUTATED     27   14
  DEL PEAK 34(19Q13.43) WILD-TYPE   35   38
        clus
vv       DEL PEAK 34(19Q13.43) MUTATED DEL PEAK 34(19Q13.43) WILD-TYPE
  FEMALE                            27                              35
  MALE                              14                              38
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(19Q13.43) MUTATED       1                         2    32
  DEL PEAK 34(19Q13.43) WILD-TYPE     3                         6    45
D55V4, multiclass
                           clus
vv                          DEL PEAK 34(19Q13.43) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                32
                           clus
vv                          DEL PEAK 34(19Q13.43) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  45
[1] 3 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 35(21Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 35(21Q11.2) MUTATED   13  7
  DEL PEAK 35(21Q11.2) WILD-TYPE 65 29
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                            20                             94 
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                             7                             29 
$`DEL PEAK 35(21Q11.2) MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M1 
       18.54        42.44        74.66         6.28        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A48R TCGA-DX-A48V TCGA-HB-A2OT TCGA-HB-A43Z 
       15.06        10.68        26.47        25.08        26.89         4.14 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
      143.41         5.92         6.28         1.05         3.91        71.70 
TCGA-PC-A5DO TCGA-UE-A6QU 
       81.01         0.72 

$`DEL PEAK 35(21Q11.2) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       23.08        70.49       108.13        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07         4.57        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        7.13        37.12        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
       13.58        73.28        22.62        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP 
        4.08        75.52        37.55         6.35        38.63        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.84        46.82        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22        18.08        27.16         8.52 

  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                          0.72                           0.07 
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                        17.820                         17.915 
[1] "0.7 - 143.4 (17.8)" "0.1 - 116.9 (17.9)"
[1] "hr=" "1"  
D56V2, continuous
D56V3, binary
                                cls
clus                              0  1
  DEL PEAK 35(21Q11.2) MUTATED   12  8
  DEL PEAK 35(21Q11.2) WILD-TYPE 50 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(21Q11.2) MUTATED     12    8
  DEL PEAK 35(21Q11.2) WILD-TYPE   50   44
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  FEMALE                           12                             50
  MALE                              8                             44
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(21Q11.2) MUTATED       1                         3    12
  DEL PEAK 35(21Q11.2) WILD-TYPE     3                         5    65
D56V4, multiclass
                           clus
vv                          DEL PEAK 35(21Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               12
                           clus
vv                          DEL PEAK 35(21Q11.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 36(21Q22.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 36(21Q22.3) MUTATED   22  9
  DEL PEAK 36(21Q22.3) WILD-TYPE 56 27
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                            31                             83 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                             9                             27 
$`DEL PEAK 36(21Q22.3) MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       14.04        27.19        18.54        42.44        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UF 
        9.70       108.13        17.10        20.05        15.06        64.18 
TCGA-DX-A48L TCGA-DX-A6BB TCGA-DX-A6BF TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IE-A4EJ 
       24.26        10.78         2.07         0.46        26.89         3.22 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        31.76       143.41         5.92        22.62         6.28 
TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A5YA TCGA-PC-A5DP TCGA-SG-A6Z7 TCGA-X6-A7WC 
       71.70        11.70         0.49        18.08         3.88        27.16 
TCGA-X6-A7WD 
        8.52 

$`DEL PEAK 36(21Q22.3) WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        12.85        24.49        46.68        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U6 
       53.26        43.04         9.04        23.08        70.49        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE 
       16.31         7.36         1.68        16.18         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       41.33         9.80        80.48        21.37         8.94         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        7.13        37.12        28.21       116.88        13.58        73.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL 
        1.05         3.91        36.39         5.26         2.37         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        6.35        38.63        81.01         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01        13.22         0.72        18.08 

  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                         18.08                          17.75 
[1] "0.5 - 143.4 (18.1)" "0.1 - 116.9 (17.8)"
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
                                cls
clus                              0  1
  DEL PEAK 36(21Q22.3) MUTATED   18 13
  DEL PEAK 36(21Q22.3) WILD-TYPE 44 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.3) MUTATED     18   13
  DEL PEAK 36(21Q22.3) WILD-TYPE   44   39
        clus
vv       DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE
  FEMALE                           18                             44
  MALE                             13                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(21Q22.3) MUTATED       1                         2    22
  DEL PEAK 36(21Q22.3) WILD-TYPE     3                         6    55
D57V4, multiclass
                           clus
vv                          DEL PEAK 36(21Q22.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               22
                           clus
vv                          DEL PEAK 36(21Q22.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 37(22Q13.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 37(22Q13.31) MUTATED   23 15
  DEL PEAK 37(22Q13.31) WILD-TYPE 55 21
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                             38                              76 
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                             15                              21 
$`DEL PEAK 37(22Q13.31) MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y 
        2.04        46.68        42.44        74.66        66.87         6.28 
TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3U9 
        8.58         9.04        23.08       108.13        42.77        14.99 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS 
       24.26        26.47        54.87         2.07        16.18         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-HS-A5NA 
        0.07         0.07         4.57        12.62        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       21.37         7.13        25.22       143.41       116.88        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-KF-A41W 
        5.92        22.62         1.05         3.91        71.70        11.70 
TCGA-SG-A6Z7 TCGA-X6-A7WB 
        3.88        18.08 

$`DEL PEAK 37(22Q13.31) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04        27.19        12.85        24.49        18.54        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       29.85         5.26        76.41        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       53.26        43.04        70.49        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        25.08        11.47        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 
        7.36         1.68         0.10        26.89         4.14        23.97 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
        0.10        80.48         8.94         3.22         1.38        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-LI-A67I 
       31.76        28.21        73.28         6.28        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       18.08         1.84        46.82        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        27.16         8.52 

  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                           0.07                            0.10 
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                         143.41                           81.01 
  DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE 
                         15.585                          18.080 
[1] "0.1 - 143.4 (15.6)" "0.1 - 81.0 (18.1)" 
[1] "hr=" "1.3"
D58V2, continuous
D58V3, binary
                                 cls
clus                               0  1
  DEL PEAK 37(22Q13.31) MUTATED   26 12
  DEL PEAK 37(22Q13.31) WILD-TYPE 36 40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(22Q13.31) MUTATED     26   12
  DEL PEAK 37(22Q13.31) WILD-TYPE   36   40
        clus
vv       DEL PEAK 37(22Q13.31) MUTATED DEL PEAK 37(22Q13.31) WILD-TYPE
  FEMALE                            26                              36
  MALE                              12                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(22Q13.31) MUTATED       1                         1    27
  DEL PEAK 37(22Q13.31) WILD-TYPE     3                         7    50
D58V4, multiclass
                           clus
vv                          DEL PEAK 37(22Q13.31) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                27
                           clus
vv                          DEL PEAK 37(22Q13.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                  50
[1] 3 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 38(XP22.33) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 38(XP22.33) MUTATED   20 15
  DEL PEAK 38(XP22.33) WILD-TYPE 58 21
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                            35                             79 
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                            15                             21 
$`DEL PEAK 38(XP22.33) MUTATED`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3UA 
       12.85        18.54         6.28        60.30         9.70        10.68 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P 
       39.35        28.80        64.18         9.73        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-FX-A2QS 
       26.47        72.72        25.08        11.47        54.87         0.46 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A4AJ 
        0.07         4.57        12.62         9.80        21.37        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A8JL 
      143.41        73.28         1.05         3.91         5.26         5.69 
TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WD 
       81.01        18.08         3.88        18.08         8.52 

$`DEL PEAK 38(XP22.33) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        27.19        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81         8.58        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48K 
       42.77         4.54        14.99        44.45        34.88        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.26        12.26        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z 
        1.68        16.18         0.10         0.07        26.89         4.14 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       23.97         0.10        41.33        80.48         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38         7.13        37.12        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58         5.92        22.62         6.28        71.70        36.39 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
       11.70         2.37         0.49         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP 
        4.08        75.52        37.55         6.35        38.63        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
        1.84        46.82        18.18        21.01        13.22         0.72 
TCGA-X6-A7WC 
       27.16 

  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                        143.41                         116.88 
  DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE 
                         14.96                          18.08 
[1] "0.1 - 143.4 (15.0)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.6"
D59V2, continuous
D59V3, binary
                                cls
clus                              0  1
  DEL PEAK 38(XP22.33) MUTATED   23 12
  DEL PEAK 38(XP22.33) WILD-TYPE 39 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(XP22.33) MUTATED     23   12
  DEL PEAK 38(XP22.33) WILD-TYPE   39   40
        clus
vv       DEL PEAK 38(XP22.33) MUTATED DEL PEAK 38(XP22.33) WILD-TYPE
  FEMALE                           23                             39
  MALE                             12                             40
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(XP22.33) MUTATED       0                         3    26
  DEL PEAK 38(XP22.33) WILD-TYPE     4                         5    51
D59V4, multiclass
                           clus
vv                          DEL PEAK 38(XP22.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               26
                           clus
vv                          DEL PEAK 38(XP22.33) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 51
[1] 3 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 39(XQ21.1) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 39(XQ21.1) MUTATED   41 16
  DEL PEAK 39(XQ21.1) WILD-TYPE 37 20
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                           57                            57 
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                           16                            20 
$`DEL PEAK 39(XQ21.1) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LW 
       27.19        42.44        74.66        60.30         9.70       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD 
       20.05        15.06        14.99        10.68        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       54.87        10.78         0.46         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        4.57        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 
        3.22         1.38        37.12        25.22       143.41        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-LI-A67I TCGA-MB-A8JL 
       22.62         6.28         3.91        71.70         5.26         5.69 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-QQ-A5VC 
        4.47         4.08        38.63        81.01        18.08        18.18 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
        0.72        18.08         8.52 

$`DEL PEAK 39(XQ21.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        24.49        18.54        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81         8.58        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB 
       70.49        17.10        17.75        42.77         4.54        44.45 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ 
       16.31         2.07         7.36         1.68        16.18         0.10 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AK 
        4.14         0.10        41.33         8.94         7.13        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PO 
       28.21       116.88        13.58         5.92         1.05        36.39 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
       11.70         2.37         0.49        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD 
       37.55         6.35        18.08         1.84        46.82        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
        3.88        13.22        27.16 

  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                         0.07                          0.10 
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE 
                        19.30                         16.18 
[1] "0.1 - 143.4 (19.3)" "0.1 - 116.9 (16.2)"
[1] "hr=" "1.5"
D60V2, continuous
D60V3, binary
                               cls
clus                             0  1
  DEL PEAK 39(XQ21.1) MUTATED   38 19
  DEL PEAK 39(XQ21.1) WILD-TYPE 24 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 39(XQ21.1) MUTATED     38   19
  DEL PEAK 39(XQ21.1) WILD-TYPE   24   33
        clus
vv       DEL PEAK 39(XQ21.1) MUTATED DEL PEAK 39(XQ21.1) WILD-TYPE
  FEMALE                          38                            24
  MALE                            19                            33
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(XQ21.1) MUTATED       2                         6    42
  DEL PEAK 39(XQ21.1) WILD-TYPE     2                         2    35
D60V4, multiclass
                           clus
vv                          DEL PEAK 39(XQ21.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              42
                           clus
vv                          DEL PEAK 39(XQ21.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 40(XQ27.1) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 40(XQ27.1) MUTATED   38 19
  DEL PEAK 40(XQ27.1) WILD-TYPE 40 17
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                           57                            57 
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                           19                            17 
$`DEL PEAK 40(XQ27.1) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R 
       27.19        12.85        18.54        46.68        42.44        74.66 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U9 TCGA-DX-A3UA 
       60.30         9.70       108.13        17.10        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O 
       39.35        28.80        34.88        64.18         9.73        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
       10.78         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ 
       23.97        41.33         9.80        80.48        21.37         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        7.13        37.12        25.22       143.41        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-MB-A8JL TCGA-MJ-A68H 
       22.62         6.28         1.05        71.70         5.69         4.47 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VC TCGA-UE-A6QU 
        6.35        38.63        81.01        18.08        18.18         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

$`DEL PEAK 40(XQ27.1) WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04         2.04        24.49        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 
       76.41        66.87         6.28        27.81         8.58        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U5 
       43.04         9.04        23.08        70.49        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48L 
       17.75        42.77         4.54        44.45        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       12.26        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK 
        0.46         0.10         0.07         0.10         8.94         1.38 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PO 
       31.76        28.21       116.88         5.92         3.91        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MO-A47R 
       11.70         5.26         2.37         0.49        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        4.08        75.52        37.55         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       21.01         3.88        13.22 

  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                       143.41                        116.88 
  DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE 
                        21.37                         14.04 
[1] "0.1 - 143.4 (21.4)" "0.1 - 116.9 (14.0)"
[1] "hr=" "1.3"
D61V2, continuous
D61V3, binary
                               cls
clus                             0  1
  DEL PEAK 40(XQ27.1) MUTATED   37 20
  DEL PEAK 40(XQ27.1) WILD-TYPE 25 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XQ27.1) MUTATED     37   20
  DEL PEAK 40(XQ27.1) WILD-TYPE   25   32
        clus
vv       DEL PEAK 40(XQ27.1) MUTATED DEL PEAK 40(XQ27.1) WILD-TYPE
  FEMALE                          37                            25
  MALE                            20                            32
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(XQ27.1) MUTATED       2                         6    38
  DEL PEAK 40(XQ27.1) WILD-TYPE     2                         2    39
D61V4, multiclass
                           clus
vv                          DEL PEAK 40(XQ27.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              38
                           clus
vv                          DEL PEAK 40(XQ27.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
