[1] "ofn"        "-oTBLCA-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/15076720/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15082908/transformed.cor.cli.txt"

nPatients in clinical file=393, in cluster file=408, common to both=389
[1]  69 389
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           98                           291 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           98                           291 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          192                           197 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          192                           197 
[1] "AMP PEAK  3(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          205                           184 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          205                           184 
[1] "AMP PEAK  4(2P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          140                           249 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          140                           249 
[1] "AMP PEAK  5(3P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          177                           212 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          177                           212 
[1] "AMP PEAK  6(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           206                            183 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           206                            183 
[1] "AMP PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           70                           319 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           70                           319 
[1] "AMP PEAK  8(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           58                           331 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           58                           331 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           193                            196 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           193                            196 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          160                           229 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          160                           229 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         33                         356 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         33                         356 
[1] "AMP PEAK 12(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           44                           345 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           44                           345 
[1] "AMP PEAK 13(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          190                           199 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          190                           199 
[1] "AMP PEAK 14(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          181                           208 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          181                           208 
[1] "AMP PEAK 15(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           118                            271 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           118                            271 
[1] "AMP PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           134                            255 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           134                            255 
[1] "AMP PEAK 17(8Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          250                           139 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          250                           139 
[1] "AMP PEAK 18(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           85                           304 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           85                           304 
[1] "AMP PEAK 19(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         172                          217 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         172                          217 
[1] "AMP PEAK 20(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          48                          341 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          48                          341 
[1] "AMP PEAK 21(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           129                            260 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           129                            260 
[1] "AMP PEAK 22(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            69                            320 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            69                            320 
[1] "AMP PEAK 23(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           125                            264 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           125                            264 
[1] "AMP PEAK 24(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         114                          275 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         114                          275 
[1] "AMP PEAK 25(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           121                            268 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           121                            268 
[1] "AMP PEAK 26(16P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            82                            307 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            82                            307 
[1] "AMP PEAK 27(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           103                            286 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           103                            286 
[1] "AMP PEAK 28(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         159                          230 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         159                          230 
[1] "AMP PEAK 29(17Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           186                            203 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           186                            203 
[1] "AMP PEAK 30(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         153                          236 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         153                          236 
[1] "AMP PEAK 31(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            147                             242 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            147                             242 
[1] "AMP PEAK 32(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            247                             142 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            247                             142 
[1] "AMP PEAK 33(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            80                            309 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            80                            309 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            85                            304 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            85                            304 
[1] "DEL PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           318 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           318 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          126                           263 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          126                           263 
[1] "DEL PEAK  4(2Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        161                         228 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        161                         228 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          198                           191 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          198                           191 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          111                           278 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          111                           278 
[1] "DEL PEAK  7(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          154                           235 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          154                           235 
[1] "DEL PEAK  8(4Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          169                           220 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          169                           220 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          190                           199 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          190                           199 
[1] "DEL PEAK 10(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           97                           292 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           97                           292 
[1] "DEL PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        182                         207 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        182                         207 
[1] "DEL PEAK 12(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        179                         210 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        179                         210 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           57                           332 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           57                           332 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          227                           162 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          227                           162 
[1] "DEL PEAK 15(8P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          238                           151 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          238                           151 
[1] "DEL PEAK 16(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        166                         223 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        166                         223 
[1] "DEL PEAK 17(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          226                           163 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          226                           163 
[1] "DEL PEAK 18(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           167                            222 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           167                            222 
[1] "DEL PEAK 19(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             70                             319 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             70                             319 
[1] "DEL PEAK 20(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            156                             233 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            156                             233 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           198                            191 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           198                            191 
[1] "DEL PEAK 22(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           145                            244 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           145                            244 
[1] "DEL PEAK 23(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         134                          255 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         134                          255 
[1] "DEL PEAK 24(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            62                            327 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            62                            327 
[1] "DEL PEAK 25(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             83                             306 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             83                             306 
[1] "DEL PEAK 26(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           148                            241 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           148                            241 
[1] "DEL PEAK 27(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           127                            262 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           127                            262 
[1] "DEL PEAK 28(15Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           149                            240 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           149                            240 
[1] "DEL PEAK 29(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           163                            226 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           163                            226 
[1] "DEL PEAK 30(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           112                            277 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           112                            277 
[1] "DEL PEAK 31(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         196                          193 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         196                          193 
[1] "DEL PEAK 32(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         169                          220 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         169                          220 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           139                            250 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           139                            250 
[1] "DEL PEAK 34(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            177                             212 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            177                             212 
[1] "DEL PEAK 35(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           87                           302 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           87                           302 
[1] "DEL PEAK 36(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            82                            307 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            82                            307 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 389 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=136,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=254,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 389 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
 [9] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  2   3 116 184  53 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     121      184       53 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  2   3 116 184  53 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     121      184       53 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
224  42  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
224  42  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
224  42  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
224  42  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=71, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=22, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.2) MUTATED    52  46
  AMP PEAK  1(1P34.2) WILD-TYPE 178 107
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           98                           285 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           46                           107 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       11.97        16.77        27.62        51.16        10.22        47.80 
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.04         5.06        17.16        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3QU 
       24.26         8.98         1.94         0.43        12.92         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
       21.86        18.41        16.70        10.59       123.85        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L 
        7.82         8.22        23.21        17.98        64.18        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE 
       15.02       166.03        15.35        38.83        17.39         0.56 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        8.09         8.94         4.01        60.66        24.30        23.41 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C0 
       19.79        12.85        22.98        15.58        19.33        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       58.92         6.15         3.06         9.67        31.07        17.23 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A3YS 
       26.93        20.12        21.40        15.81        14.07        24.92 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A767 
        0.49         7.73        20.98         7.36        10.92         4.73 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WV 
       32.98        21.34        19.07        22.72        38.60        21.24 
TCGA-K4-A5RI TCGA-K4-A6MB TCGA-MV-A51V TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
       11.70        15.42        13.48        22.68        86.83        65.75 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-AAML TCGA-XF-AAMY 
        3.58        17.82         4.54        97.45         7.63        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       44.32        86.30        18.81        13.64        30.28        74.56 
TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        3.48        20.22        19.69        63.02        38.73        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA5H 
       19.40        19.17 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       41.75        66.54        15.12        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        2.66         6.74        12.39         6.58        13.15        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        8.35         8.25        16.18         4.67        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41        23.01         0.46         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO 
       12.10        11.34        11.34        11.87        13.08         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        7.20         5.46        16.31         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
       15.62         1.81         7.79        87.32         2.20        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       30.67        13.58        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        43.59        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         2.24        16.70         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04        12.62        22.52        27.98        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        25.74        46.78        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        27.45         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       62.86        18.81        12.69        12.36         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       10.85         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        15.95        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       17.62        66.02         6.94        64.44        19.46         2.24 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
        4.50        15.91        17.75         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         2.20        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
       20.05         5.62        10.65         7.00        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
        3.45         2.76         9.14        27.68         9.07         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         6.38        11.80        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       31.56        17.62        37.05        76.01        67.79       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       35.24        29.56         1.64        45.04         6.58       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
        6.77        56.48        30.94        61.45        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       13.41        52.73        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 
       34.06         8.61        59.38        60.16        57.90         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                        18.61                         14.56 
[1] "0.4 - 166.0 (18.6)" "0.1 - 140.8 (14.6)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1P34.2) MUTATED         0       29        27       39
  AMP PEAK  1(1P34.2) WILD-TYPE       4       95       100       90
D1V3, multiclass
           clus
vv          AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           29                            95
  STAGE III                          27                           100
  STAGE IV                           39                            90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  1(1P34.2) MUTATED         33  45  14
  AMP PEAK  1(1P34.2) WILD-TYPE       88 139  39
D1V4, multiclass
          clus
vv         AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1+T2                          33                            88
  T3                                45                           139
  T4                                14                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  1(1P34.2) MUTATED    44  16  23   3
  AMP PEAK  1(1P34.2) WILD-TYPE 180  26  52   5
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          44                           180
  N1                          16                            26
  N2                          23                            52
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    42   2
  AMP PEAK  1(1P34.2) WILD-TYPE 143   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     42    2
  AMP PEAK  1(1P34.2) WILD-TYPE  143    8
   clus
vv  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  0                          42                           143
  1                           2                             8
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    27  71
  AMP PEAK  1(1P34.2) WILD-TYPE  74 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     27   71
  AMP PEAK  1(1P34.2) WILD-TYPE   74  217
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                          27                            74
  MALE                            71                           217
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       4                         6    83
  AMP PEAK  1(1P34.2) WILD-TYPE    38                        15   228
D1V11, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              83
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     3  87
  AMP PEAK  1(1P34.2) WILD-TYPE   6 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      3   87
  AMP PEAK  1(1P34.2) WILD-TYPE    6  265
                        clus
vv                       AMP PEAK  1(1P34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  1(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           265
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   113  78
  AMP PEAK  2(1Q21.3) WILD-TYPE 117  75
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          191                           192 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           78                            75 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W 
       22.29         8.35        16.27        16.83        16.77        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J 
        0.62        41.75        15.12        10.22        47.80         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        6.74        19.04        32.84         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        17.16        16.18        20.48        28.70         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A3KJ 
        1.94         0.43        12.46        11.34        11.34         5.46 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC 
        5.19         1.84        21.86         2.14        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
      112.44         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
       13.58         7.82         8.22        21.30        23.21        48.00 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       17.98        67.36        15.68        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA77 
      166.03        12.36        10.49         8.65        13.64        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
        0.56         0.66        12.99         1.22        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        8.09         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y 
        5.52        19.79        12.85        22.98        27.35        15.58 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC 
       11.01        19.33        27.45        18.08         6.28         6.15 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       12.36         2.27         4.31         9.67        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY 
       17.23         3.25         6.48        33.01        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       66.02        19.46        21.40        15.81         4.50        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       24.92         0.49        13.91         7.73         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
        7.36        10.92        20.05        10.65        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
       21.34        19.10        19.82        20.28        10.59         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
       25.02         9.14        11.70         1.74        15.42        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        13.48        12.23         3.75        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PB TCGA-UY-A9PD 
       17.62        37.05        22.68        86.83        29.56        17.82 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI 
        6.58        97.45        15.35        17.88        48.62        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG 
        3.22        11.90        66.64         2.10        13.74       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
        7.63        71.57         2.96         6.77        98.99        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       61.45        86.30        18.81         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       18.64        30.28        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       52.73        20.22        34.06        19.69        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       38.73        35.41        57.90        47.15        19.17 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7R 
       11.97        91.63       103.50       105.70        44.94        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 
       34.98        49.12        51.16        66.54        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.50        14.96         8.25         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       17.56        24.26        28.41        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        7.20        16.31        13.58        66.41        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.14        17.62        15.62        87.32        17.72        50.27 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 
       76.60        41.06        30.67         7.53        43.50        12.03 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70        17.39        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.92        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN 
        8.94        33.04        12.62        22.52        27.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       25.74        46.78        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       53.88         5.36         5.69         8.25        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
        7.10        13.35        62.86        18.81        12.69         3.06 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.85         7.13         8.94        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 
       26.93        35.24         7.23         6.94        64.44         2.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.91        14.07         8.94         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31         7.63        27.09         5.62         4.73         7.00 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
        8.48        27.35        19.40         8.22         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT 
        2.76        27.68         9.07         1.81         6.38        21.07 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P 
       16.67        14.24         1.84        12.43        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75         3.58       112.83        35.24         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL 
       45.04       125.49        97.12         1.87        64.80        66.41 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        16.27        92.98        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         8.32        44.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        3.88        18.84         9.63         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       27.19        28.41        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.61        60.16        19.40         8.52         5.52        10.13 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.10                          0.46 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        15.58                         15.93 
[1] "0.1 - 166.0 (15.6)" "0.5 - 140.8 (15.9)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED         1       62        53       73
  AMP PEAK  2(1Q21.3) WILD-TYPE       3       62        74       56
D2V3, multiclass
           clus
vv          AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                             1                             3
  STAGE II                           62                            62
  STAGE III                          53                            74
  STAGE IV                           73                            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED         59 91 25
  AMP PEAK  2(1Q21.3) WILD-TYPE       62 93 28
D2V4, multiclass
          clus
vv         AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1+T2                          59                            62
  T3                                91                            93
  T4                                25                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  2(1Q21.3) MUTATED    96  26  41   6
  AMP PEAK  2(1Q21.3) WILD-TYPE 128  16  34   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          96                           128
  N1                          26                            16
  N2                          41                            34
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   88  7
  AMP PEAK  2(1Q21.3) WILD-TYPE 97  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     88    7
  AMP PEAK  2(1Q21.3) WILD-TYPE   97    3
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          88                            97
  1                           7                             3
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    49 143
  AMP PEAK  2(1Q21.3) WILD-TYPE  52 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     49  143
  AMP PEAK  2(1Q21.3) WILD-TYPE   52  145
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          49                            52
  MALE                           143                           145
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED      15                        10   157
  AMP PEAK  2(1Q21.3) WILD-TYPE    27                        11   154
D2V11, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             157
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                27
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     4 171
  AMP PEAK  2(1Q21.3) WILD-TYPE   5 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      4  171
  AMP PEAK  2(1Q21.3) WILD-TYPE    5  181
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         171
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           181
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q23.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q23.3) MUTATED   124  79
  AMP PEAK  3(1Q23.3) WILD-TYPE 106  74
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          203                           180 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                           79                            74 
$`AMP PEAK  3(1Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O 
       22.29        11.97       105.70         8.35        16.27        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.77        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        10.22        47.80        40.08         2.66         6.74 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
       19.04        32.84        14.89         5.06         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       16.18        20.48         4.67        12.82         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY 
        8.98         1.94         0.43        12.46        11.34        11.34 
TCGA-CF-A9FF TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       11.87         7.20         5.46         1.84        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       130.88       112.44        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20        13.58         7.82         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 
       21.30        23.21        48.00        17.98        67.36        15.68 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        10.62        43.59        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7DV 
        0.49        17.39         0.56         0.66        12.99         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA 
       13.68        12.95         8.09        16.77         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       24.30        23.41        17.98         5.52        25.74        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT 
       12.85        22.98        27.35         3.62        15.58        11.01 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       19.33        27.45         6.28         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.31         9.67        31.07        10.65        17.23         3.25 
TCGA-G2-A2EF TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO 
       61.94        17.62        66.02        19.46        21.40        15.81 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         0.49        13.91         7.73         2.10 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO 
       20.98         7.36        10.92        20.05         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       10.59        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RH 
        3.06         9.01        25.02         3.45         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
       11.70         1.74        15.42        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       13.48        12.23         3.75        31.56        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD 
       86.83         3.58        17.82         4.54         6.58        97.45 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SW 
       15.35        17.88        48.62        79.66         3.22        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML 
       28.24        66.64         2.10        13.74       110.60         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       71.57         2.96         6.77        98.99        44.32        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       86.30        27.06        18.81         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       18.64        30.28        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       52.73        20.22        34.06        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       35.41        57.90        47.15        19.17        10.13 

$`AMP PEAK  3(1Q23.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       91.63       103.50        44.94        34.98        49.12        66.54 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       33.83         7.33        12.39         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42B 
       17.88        19.50         5.06        14.96         8.25        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       24.26        28.41        23.01         0.46         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL 
       12.10        13.08        12.92         4.90         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58        66.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62         1.81        17.72         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 
      140.81        64.18        41.56        76.60        41.06        30.67 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4XJ 
        8.65         7.53        43.50        12.03        15.35         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
       16.70        14.56        13.97        14.33         0.92        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
       15.32        14.37        32.02         8.94        33.04        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98        29.16        46.78        14.96        20.91 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88         5.36         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         7.10        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A61P 
       12.69         2.27        10.85         7.13         8.94         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       20.12         6.94        64.44         2.24         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       14.07         8.94         3.12         2.20        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QK 
        7.63        27.09         5.62         7.00         8.48        27.35 
TCGA-GV-A40E TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ 
        8.58         8.22        21.24         2.76        27.68         1.81 
TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
        6.38        21.07        16.67        14.24         1.84        12.43 
TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       17.62        76.01        67.79        65.75       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       29.56         1.64        45.04       125.49        97.12         1.87 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        66.41        12.76        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24        16.27        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN5 
       54.90        91.73         8.32        30.94        61.45        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        3.88        18.84         9.63         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       27.19        28.41        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       19.69         8.61        60.16        19.40         8.52         5.52 

  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                         0.10                          0.46 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                       15.680                        15.765 
[1] "0.1 - 166.0 (15.7)" "0.5 - 140.8 (15.8)"
[1] "hr=" "1"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(1Q23.3) MUTATED         2       64        57       79
  AMP PEAK  3(1Q23.3) WILD-TYPE       2       60        70       50
D3V3, multiclass
           clus
vv          AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           64                            60
  STAGE III                          57                            70
  STAGE IV                           79                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  3(1Q23.3) MUTATED         68 94 27
  AMP PEAK  3(1Q23.3) WILD-TYPE       53 90 26
D3V4, multiclass
          clus
vv         AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  T0+T1+T2                          68                            53
  T3                                94                            90
  T4                                27                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  3(1Q23.3) MUTATED   104  27  43   8
  AMP PEAK  3(1Q23.3) WILD-TYPE 120  15  32   0
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  N0                         104                           120
  N1                          27                            15
  N2                          43                            32
  N3                           8                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q23.3) MUTATED   93  7
  AMP PEAK  3(1Q23.3) WILD-TYPE 92  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     93    7
  AMP PEAK  3(1Q23.3) WILD-TYPE   92    3
   clus
vv  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  0                          93                            92
  1                           7                             3
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED    50 155
  AMP PEAK  3(1Q23.3) WILD-TYPE  51 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     50  155
  AMP PEAK  3(1Q23.3) WILD-TYPE   51  133
        clus
vv       AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  FEMALE                          50                            51
  MALE                           155                           133
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q23.3) MUTATED      16                        14   165
  AMP PEAK  3(1Q23.3) WILD-TYPE    26                         7   146
D3V11, multiclass
                           clus
vv                          AMP PEAK  3(1Q23.3) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             165
                           clus
vv                          AMP PEAK  3(1Q23.3) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED     4 182
  AMP PEAK  3(1Q23.3) WILD-TYPE   5 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED      4  182
  AMP PEAK  3(1Q23.3) WILD-TYPE    5  170
                        clus
vv                       AMP PEAK  3(1Q23.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         182
                        clus
vv                       AMP PEAK  3(1Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           170
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P25.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P25.1) MUTATED    82  56
  AMP PEAK  4(2P25.1) WILD-TYPE 148  97
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          138                           245 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           56                            97 
$`AMP PEAK  4(2P25.1) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.77        17.16         0.62        41.75        51.16        15.12 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       12.39        13.15        19.04        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
        5.06         8.35        16.18        20.48        12.82        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
       28.41         8.98        23.01         0.43         0.69        12.62 
TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       12.10        11.34         7.20        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       18.41       130.88       112.44        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        2.20         7.82         8.22        48.00        17.98        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       67.36        15.68        30.67        38.24        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       12.36        10.49         8.65        12.03        10.62        43.59 
TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       17.39        12.99         8.09         8.94        60.66        24.30 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ 
       46.78        19.79        12.85        27.35        20.91        27.45 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        7.10         6.28         6.15        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A3VY 
        4.31        10.85        17.23         3.25         6.48        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       66.02        19.46         4.50        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP 
        7.73         2.10        20.98        20.05        10.65        32.98 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA 
       21.34        20.28         8.48        10.59        27.35        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI 
       19.40        38.60         8.22        25.02        21.24        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-MV-A51V TCGA-UY-A78K 
        1.81        15.42         6.38        11.80        13.48        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HD 
       22.68        65.75       112.83        17.82         4.54        97.45 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 
       15.35         1.87        48.62        12.76        28.24        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN2 
       66.64       110.60         7.63         6.77        44.32        61.45 
TCGA-XF-AAN8 TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RC TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.88        18.64        24.13        74.56        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       34.06        19.69        59.38        38.73        19.40         8.52 

$`AMP PEAK  4(2P25.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.27        44.94        16.83        34.98        27.62        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.74         6.58        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         8.25        17.16         4.67         9.96        17.56 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       24.26         1.94         0.46        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A9FF 
       12.10        12.26        13.12        12.00        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        13.58        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62         1.81       123.85        13.58        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA71 
       41.56        76.60        41.06        13.58         7.53        13.64 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.50        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.32        14.37        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.62        22.52        27.98        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
        5.52        25.74        22.98        14.96         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
        8.25        18.08        58.92         2.70        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       18.81        12.69         9.67        31.07         7.13        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM 
       33.01         7.23        20.12         6.94        64.44        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        2.24        15.81        15.91        17.75        24.92         0.49 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        27.09         5.62         4.73         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF 
       19.10        19.82         8.58        19.07         1.51         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        9.01         3.45         2.76         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        31.56        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        76.01        67.79         3.58        35.24        29.56 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
        1.64        45.04         6.58       125.49        97.12        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66         3.22        66.41        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       92.98        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 
        2.96         8.32        98.99        56.48        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       11.97        13.64         7.36        21.11        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       82.49         2.89         8.61        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        47.15        19.17         5.52        10.13 

  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                       16.965                        15.580 
[1] "0.4 - 166.0 (17.0)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(2P25.1) MUTATED         1       39        38       58
  AMP PEAK  4(2P25.1) WILD-TYPE       3       85        89       71
D4V3, multiclass
           clus
vv          AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  STAGE I                             1                             3
  STAGE II                           39                            85
  STAGE III                          38                            89
  STAGE IV                           58                            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  4(2P25.1) MUTATED         43  66  19
  AMP PEAK  4(2P25.1) WILD-TYPE       78 118  34
D4V4, multiclass
          clus
vv         AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  T0+T1+T2                          43                            78
  T3                                66                           118
  T4                                19                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  4(2P25.1) MUTATED    69  20  33   5
  AMP PEAK  4(2P25.1) WILD-TYPE 155  22  42   3
D4V5, multiclass
    clus
vv   AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  N0                          69                           155
  N1                          20                            22
  N2                          33                            42
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    61   5
  AMP PEAK  4(2P25.1) WILD-TYPE 124   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     61    5
  AMP PEAK  4(2P25.1) WILD-TYPE  124    5
   clus
vv  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  0                          61                           124
  1                           5                             5
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    45  95
  AMP PEAK  4(2P25.1) WILD-TYPE  56 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     45   95
  AMP PEAK  4(2P25.1) WILD-TYPE   56  193
        clus
vv       AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  FEMALE                          45                            56
  MALE                            95                           193
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P25.1) MUTATED      10                         9   115
  AMP PEAK  4(2P25.1) WILD-TYPE    32                        12   196
D4V11, multiclass
                           clus
vv                          AMP PEAK  4(2P25.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             115
                           clus
vv                          AMP PEAK  4(2P25.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED     4 122
  AMP PEAK  4(2P25.1) WILD-TYPE   5 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED      4  122
  AMP PEAK  4(2P25.1) WILD-TYPE    5  230
                        clus
vv                       AMP PEAK  4(2P25.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       AMP PEAK  4(2P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           230
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3P25.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(3P25.2) MUTATED   110  63
  AMP PEAK  5(3P25.2) WILD-TYPE 120  90
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          173                           210 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                           63                            90 
$`AMP PEAK  5(3P25.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97       105.70         8.35        16.27        44.94 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.77        17.16        27.62         0.62        15.12        47.80 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       40.08         7.33         2.66        12.39        32.84         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C 
       17.16        16.18        20.48         4.67         9.96        28.70 
TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.46         4.90         7.20         5.19        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
       21.86         2.14        66.41        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN 
        1.81        10.59       123.85        87.32         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       50.27        23.21        48.00        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 
       41.06        30.67        15.02       166.03        10.49        13.64 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 
       10.62        15.35        38.83         0.10         0.49        17.39 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
        0.56        12.99         1.22        13.68        12.95         8.09 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43N TCGA-FD-A43P 
        8.94        33.04        24.30        23.41        22.98        27.35 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TD 
       20.91         5.36        18.08         7.10         6.28        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO 
       10.65        17.23         3.25         6.48        61.94        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       33.01        20.12        17.62        66.02        64.44        19.46 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.81         4.50        14.07         0.49        13.91         2.10 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO 
       20.98         2.20         7.36        10.92         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
       10.59        27.35        19.07        22.72         1.51        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO 
       25.02         3.45        21.24         9.07        15.42        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        13.48        12.23        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OC 
       12.43        17.62        37.05        86.83        76.01         3.58 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF 
       29.56        17.82         4.54         6.58        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV 
       15.35         1.87        48.62        79.66         3.22        12.76 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX 
        2.10        10.82       110.60         7.63        71.57         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       98.99        44.32        18.64        30.28        28.41        74.56 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       52.73        82.49        47.84        19.69        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5P 
       38.73        35.41        57.90        19.40        10.13 

$`AMP PEAK  5(3P25.2) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 
       91.63       103.50        16.83        34.98        49.12        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A3JM TCGA-BT-A0S7 
       51.16        66.54        10.22        33.83         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A42B 
       14.89        14.96         5.06         8.25        12.82        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
       24.26        28.41         8.98         1.94        23.01         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA 
       11.87        13.08        12.92         5.46        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.70        16.14        17.62        15.62         7.79         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       13.58        17.72        21.30         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6Q 
      140.81        41.56        76.60        67.36        38.24        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC 
       12.36         8.65         7.53        43.50        12.03        43.59 
TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       24.66         2.24        16.70         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       14.33         0.92        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       16.77         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       12.85        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       11.01        19.33         5.69         8.25        27.45        58.92 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TK 
        2.70        13.35        62.86        18.81         6.15        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        7.13         8.94        30.61        15.95        26.93         7.23 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        6.94        21.40         2.24        15.91        17.75        24.92 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        8.94         7.73         3.12        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A40E 
       27.09        20.05         5.62         7.00        19.10         8.58 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC 
       19.40         3.06         9.01         8.22         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT 
       27.68        11.70         1.74         1.81         6.38        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB 
       16.67         3.75        31.56        22.68        67.79        65.75 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HI 
      112.83        35.24         1.64        45.04       125.49        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       92.98        11.31        54.90        91.73         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64         7.36        21.11        24.13        27.19        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       13.41         3.48        52.60        20.22         2.89        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
        8.61        60.16         8.52        47.15        19.17         5.52 

  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                         0.10                          0.43 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                        16.27                         15.14 
[1] "0.1 - 166.0 (16.3)" "0.4 - 140.8 (15.1)"
[1] "hr=" "1.3"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(3P25.2) MUTATED         2       53        53       67
  AMP PEAK  5(3P25.2) WILD-TYPE       2       71        74       62
D5V3, multiclass
           clus
vv          AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           53                            71
  STAGE III                          53                            74
  STAGE IV                           67                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  5(3P25.2) MUTATED         53  78  30
  AMP PEAK  5(3P25.2) WILD-TYPE       68 106  23
D5V4, multiclass
          clus
vv         AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  T0+T1+T2                          53                            68
  T3                                78                           106
  T4                                30                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  5(3P25.2) MUTATED    89  17  45   5
  AMP PEAK  5(3P25.2) WILD-TYPE 135  25  30   3
D5V5, multiclass
    clus
vv   AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  N0                          89                           135
  N1                          17                            25
  N2                          45                            30
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED    82   5
  AMP PEAK  5(3P25.2) WILD-TYPE 103   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED     82    5
  AMP PEAK  5(3P25.2) WILD-TYPE  103    5
   clus
vv  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  0                          82                           103
  1                           5                             5
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED    32 145
  AMP PEAK  5(3P25.2) WILD-TYPE  69 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED     32  145
  AMP PEAK  5(3P25.2) WILD-TYPE   69  143
        clus
vv       AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  FEMALE                          32                            69
  MALE                           145                           143
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3P25.2) MUTATED      13                         6   154
  AMP PEAK  5(3P25.2) WILD-TYPE    29                        15   157
D5V11, multiclass
                           clus
vv                          AMP PEAK  5(3P25.2) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             154
                           clus
vv                          AMP PEAK  5(3P25.2) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED     3 161
  AMP PEAK  5(3P25.2) WILD-TYPE   6 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED      3  161
  AMP PEAK  5(3P25.2) WILD-TYPE    6  191
                        clus
vv                       AMP PEAK  5(3P25.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         161
                        clus
vv                       AMP PEAK  5(3P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           191
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(3Q26.33) MUTATED   121  82
  AMP PEAK  6(3Q26.33) WILD-TYPE 109  71
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           203                            180 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                            82                             71 
$`AMP PEAK  6(3Q26.33) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S 
       22.29       103.50         8.35        16.27        16.77        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       27.62         0.62        15.12        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R 
        6.74        12.39        13.15        19.04        32.84         5.06 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82         9.96        28.70        24.26         0.46         0.43 
TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       12.00        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84        21.86        66.41        18.41       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS 
       16.14         1.81        10.59         2.20         7.82        50.27 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       23.21        48.00        17.98        64.18        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U 
       30.67        38.24        15.02        13.58       166.03        10.49 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       15.35         0.10         0.49        17.39         0.56        12.99 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.22        13.68        12.95         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P 
       33.04        22.52        60.66        24.30        23.41        27.35 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 
       20.91        15.58        19.33         5.36         8.25        18.08 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        7.10         6.28         6.15        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.31         9.67        10.65         6.48        61.94        30.61 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       35.24        33.01         7.23        17.62        66.02        64.44 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OS TCGA-GD-A76B 
       24.92         0.49         8.94        13.91        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       10.92        11.31         7.63         4.73        10.65         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72        19.40        38.60         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
       25.02         3.45        21.24         9.07        11.70        15.42 
TCGA-K4-AAQO TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       11.80        12.23        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB 
       17.62        37.05        86.83        65.75         3.58        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       17.82        45.04         6.58        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SZ 
        1.87        17.88        79.66         3.22        12.76        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ 
       26.27        66.64        13.74       110.60         7.63        71.57 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN4 
        2.96         6.77        98.99        44.32        86.30        27.06 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       13.64        18.64        21.11        30.28        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       35.41        57.90        19.40        19.17        10.13 

$`AMP PEAK  6(3Q26.33) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        91.63       105.70        44.94        16.83        17.16 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       49.12        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       33.83         6.58        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       14.96        20.48        17.56        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.62        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       11.87        13.08         5.19        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.70        17.62        15.62         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         8.22        17.72        21.30         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6T 
       10.55       140.81        41.56        76.60        67.36        12.36 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
        7.53        38.83        24.66         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 
       14.56        13.97        14.33         0.92        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM 
       14.37         8.94         4.01        12.62        27.98        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       22.98        14.96         3.62        26.73        53.88        11.01 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
        5.69        27.45        58.92         2.70        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       18.81        12.69        10.85        31.07         7.13        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3C 
        8.94         3.25        15.95        26.93        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
       19.46        21.40         7.73         2.10         3.12         2.20 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV 
       11.31        27.09        20.05         5.62        32.98        14.27 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A4AC 
       19.82         8.58         1.51         3.06         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       27.68         1.74         1.81         6.38        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O 
       21.07        13.48        16.67         3.75        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HE 
       67.79       112.83        35.24         4.54         1.64       125.49 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       48.62        64.80        66.41        11.90        23.64        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       11.31        54.90        91.73         8.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       61.45        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66        11.97         7.36        24.13        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4U TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       28.41        82.49         8.61         8.52        47.15         5.52 

  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                          0.10                           0.66 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                         16.14                          15.32 
[1] "0.1 - 166.0 (16.1)" "0.7 - 140.8 (15.3)"
[1] "hr=" "1"  
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(3Q26.33) MUTATED         2       60        70       70
  AMP PEAK  6(3Q26.33) WILD-TYPE       2       64        57       59
D6V3, multiclass
           clus
vv          AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            60                             64
  STAGE III                           70                             57
  STAGE IV                            70                             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK  6(3Q26.33) MUTATED         55 105  28
  AMP PEAK  6(3Q26.33) WILD-TYPE       66  79  25
D6V4, multiclass
          clus
vv         AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  T0+T1+T2                           55                             66
  T3                                105                             79
  T4                                 28                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  6(3Q26.33) MUTATED   110  20  47   5
  AMP PEAK  6(3Q26.33) WILD-TYPE 114  22  28   3
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  N0                          110                            114
  N1                           20                             22
  N2                           47                             28
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.33) MUTATED   96  6
  AMP PEAK  6(3Q26.33) WILD-TYPE 89  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED     96    6
  AMP PEAK  6(3Q26.33) WILD-TYPE   89    4
   clus
vv  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  0                           96                             89
  1                            6                              4
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED    55 151
  AMP PEAK  6(3Q26.33) WILD-TYPE  46 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED     55  151
  AMP PEAK  6(3Q26.33) WILD-TYPE   46  137
        clus
vv       AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  FEMALE                           55                             46
  MALE                            151                            137
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.33) MUTATED      14                        10   175
  AMP PEAK  6(3Q26.33) WILD-TYPE    28                        11   136
D6V11, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.33) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              175
                           clus
vv                          AMP PEAK  6(3Q26.33) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED     5 187
  AMP PEAK  6(3Q26.33) WILD-TYPE   4 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED      5  187
  AMP PEAK  6(3Q26.33) WILD-TYPE    4  165
                        clus
vv                       AMP PEAK  6(3Q26.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          187
                        clus
vv                       AMP PEAK  6(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4P16.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(4P16.3) MUTATED    49  18
  AMP PEAK  7(4P16.3) WILD-TYPE 181 135
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           67                           316 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           18                           135 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA87 TCGA-BT-A20P 
       11.97       105.70        17.16        49.12        47.80        17.88 
TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V 
       14.89        12.82         1.94        23.01         0.69        12.46 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3KJ TCGA-CU-A5W6 
       12.62        12.00        11.34        11.87         5.46         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM 
        2.14        66.41       130.88         7.79        87.32         7.82 
TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A541 
       50.27        64.18        67.36        12.03        38.83        17.39 
TCGA-E7-A5KE TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A5BV TCGA-FD-A5BZ 
        0.56         0.92        60.66        23.41         5.36        27.45 
TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY 
       58.92         6.15        12.36        35.24        33.01        17.62 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GD-A76B TCGA-GU-A42R TCGA-GV-A6ZA 
       66.02        21.40        15.91         7.36        11.31        22.72 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB 
        1.51         9.01        25.02         9.14         1.81        15.42 
TCGA-MV-A51V TCGA-UY-A78N TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMY TCGA-XF-AAMZ 
       13.48        86.83        28.24         2.24        98.99        44.32 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA51 
       11.97        13.64        21.11        52.60         8.61        38.73 
TCGA-ZF-AA5H 
       19.17 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        91.63       103.50         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        16.77        34.98        27.62         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 
       51.16        66.54        15.12        10.22        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        32.84        12.16        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        8.98         0.46         0.43        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN 
       12.26        13.12        12.10        11.34        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.19        16.31        13.58        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59       123.85         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        17.72        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         2.24        16.70         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       12.99        14.33         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       33.04         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25         6.48        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       26.93         7.23        20.12         6.94        64.44        19.46 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81         4.50        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        10.92        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
       10.59        27.35         8.58        19.07        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        3.06         8.22         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        9.07        11.70         1.74         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        21.07        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       11.90        23.64        21.04        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32         6.77        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        18.64         7.36        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        60.16        63.02        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15         5.52        10.13 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         0.56                          0.10 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       130.88                        166.03 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                        15.91                         15.65 
[1] "0.6 - 130.9 (15.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.7"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(4P16.3) MUTATED         0       31        21       17
  AMP PEAK  7(4P16.3) WILD-TYPE       4       93       106      112
D7V3, multiclass
           clus
vv          AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           31                            93
  STAGE III                          21                           106
  STAGE IV                           17                           112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  7(4P16.3) MUTATED         31  29   8
  AMP PEAK  7(4P16.3) WILD-TYPE       90 155  45
D7V4, multiclass
          clus
vv         AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  T0+T1+T2                          31                            90
  T3                                29                           155
  T4                                 8                            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"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  7(4P16.3) MUTATED    49   7   8   2
  AMP PEAK  7(4P16.3) WILD-TYPE 175  35  67   6
D7V5, multiclass
    clus
vv   AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  N0                          49                           175
  N1                           7                            35
  N2                           8                            67
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    43   1
  AMP PEAK  7(4P16.3) WILD-TYPE 142   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     43    1
  AMP PEAK  7(4P16.3) WILD-TYPE  142    9
   clus
vv  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  0                          43                           142
  1                           1                             9
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    19  51
  AMP PEAK  7(4P16.3) WILD-TYPE  82 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     19   51
  AMP PEAK  7(4P16.3) WILD-TYPE   82  237
        clus
vv       AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  FEMALE                          19                            82
  MALE                            51                           237
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P16.3) MUTATED      12                         2    50
  AMP PEAK  7(4P16.3) WILD-TYPE    30                        19   261
D7V11, multiclass
                           clus
vv                          AMP PEAK  7(4P16.3) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              50
                           clus
vv                          AMP PEAK  7(4P16.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     2  60
  AMP PEAK  7(4P16.3) WILD-TYPE   7 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      2   60
  AMP PEAK  7(4P16.3) WILD-TYPE    7  292
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           292
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(4Q13.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(4Q13.3) MUTATED    37  21
  AMP PEAK  8(4Q13.3) WILD-TYPE 193 132
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           58                           325 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           21                           132 
$`AMP PEAK  8(4Q13.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-BT-A20N TCGA-BT-A2LD 
       16.27        27.62         0.62        51.16        32.84        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A8HX 
        9.96        28.70        24.26        23.01        12.62        11.34 
TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-DK-A2I6 
       11.34         5.46         2.14        18.41         7.79        87.32 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A541 
       48.00        17.98        64.18        67.36        38.83        17.39 
TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
       60.66        19.79        15.58         5.36        27.45        18.08 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EJ TCGA-G2-A3VY TCGA-G2-AA3B 
       13.35         6.15        12.36        30.61        17.62        66.02 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JW 
       17.75         0.49         7.73         7.36        10.92        21.34 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K 
       22.72         9.01        21.24        15.58        13.48        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A9T4 TCGA-XF-AAMZ TCGA-YF-AA3L 
       37.05        76.01       112.83        16.27        44.32        11.97 
TCGA-ZF-A9R2 TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA5H 
       21.11        20.22        19.69        19.17 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
       16.18         4.67        12.82        17.56        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       11.87        13.08        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         1.84        13.58        21.86        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81        10.59       123.85         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       20.81        10.55       140.81        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       14.07        12.95        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69         8.25        58.92         2.70         7.10         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25         6.48        61.94        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D 
       35.24        33.01         7.23        20.12         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        24.92         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         8.22        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        11.80        15.32        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M 
       14.24         1.84         3.75        12.43        31.56        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        67.79        65.75         3.58        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         4.54         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      125.49        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        9.63         0.66        13.64        18.64         7.36        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
        3.48        52.73        52.60        82.49        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       35.41        57.90        19.40         8.52        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                       112.83                        166.03 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                       18.245                        15.020 
[1] "0.5 - 112.8 (18.2)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.3"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(4Q13.3) MUTATED         0       25        14       19
  AMP PEAK  8(4Q13.3) WILD-TYPE       4       99       113      110
D8V3, multiclass
           clus
vv          AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           25                            99
  STAGE III                          14                           113
  STAGE IV                           19                           110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  8(4Q13.3) MUTATED         24  24   4
  AMP PEAK  8(4Q13.3) WILD-TYPE       97 160  49
D8V4, multiclass
          clus
vv         AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  T0+T1+T2                          24                            97
  T3                                24                           160
  T4                                 4                            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"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  8(4Q13.3) MUTATED    35   8  10   1
  AMP PEAK  8(4Q13.3) WILD-TYPE 189  34  65   7
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  N0                          35                           189
  N1                           8                            34
  N2                          10                            65
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    30   0
  AMP PEAK  8(4Q13.3) WILD-TYPE 155  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     30    0
  AMP PEAK  8(4Q13.3) WILD-TYPE  155   10
   clus
vv  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  0                          30                           155
  1                           0                            10
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    23  35
  AMP PEAK  8(4Q13.3) WILD-TYPE  78 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     23   35
  AMP PEAK  8(4Q13.3) WILD-TYPE   78  253
        clus
vv       AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  FEMALE                          23                            78
  MALE                            35                           253
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(4Q13.3) MUTATED       5                         3    45
  AMP PEAK  8(4Q13.3) WILD-TYPE    37                        18   266
D8V11, multiclass
                           clus
vv                          AMP PEAK  8(4Q13.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              45
                           clus
vv                          AMP PEAK  8(4Q13.3) WILD-TYPE
  ASIAN                                                37
  BLACK OR AFRICAN AMERICAN                            18
  WHITE                                               266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     2  49
  AMP PEAK  8(4Q13.3) WILD-TYPE   7 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      2   49
  AMP PEAK  8(4Q13.3) WILD-TYPE    7  303
                        clus
vv                       AMP PEAK  8(4Q13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          49
                        clus
vv                       AMP PEAK  8(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(5P15.33) MUTATED   115  75
  AMP PEAK  9(5P15.33) WILD-TYPE 115  78
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           190                            193 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            75                             78 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
      105.70         8.35        16.27        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20P TCGA-BT-A20T 
       41.75        10.22         6.74        12.39        17.88        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         8.35        17.16        12.82         9.96        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A5UA 
       24.26         8.98        23.01         0.43        10.95        12.00 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD 
       12.92         7.20         5.19         1.84        21.86       112.44 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85        87.32         7.82         8.22        23.21         9.67 
TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       10.55        64.18        67.36        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       15.02        13.58       166.03        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        12.03        15.35        38.83        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q 
        0.49        17.39        12.99         1.22        12.95         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       32.02        16.77         8.94        22.52        60.66        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR 
       29.16         5.52        25.74        19.79        15.58        26.73 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         5.36         8.25        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        3.06         4.31        10.85        17.23         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        35.24         7.23        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS 
       14.07        24.92         0.49        13.91         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.36        10.92         7.63         5.62         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       10.59         8.58        19.07        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
        9.01         8.22         2.76         9.14         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
        1.81        15.42        15.32        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB 
        1.84        31.56        17.62        37.05        86.83        65.75 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SG 
      112.83        29.56         4.54         6.58        97.12        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 
       79.66         3.22        23.64        28.24        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ 
       66.64         2.10        92.98        10.82       110.60        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
        7.63         2.96         6.77        86.30        18.81        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RG 
       21.11        24.13        30.28        21.86        74.56        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
        8.52        47.15        19.17        10.13 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        11.97        91.63       103.50        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       16.77        17.16        34.98        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 
       47.80        33.83        40.08         7.33         2.66         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        32.84        12.16        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         8.25        16.18        20.48         4.67        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
       28.41         1.94         0.46         0.69        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
       11.34        11.87        13.08         4.90         5.46        16.31 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        7.79         2.20        13.58        17.72        50.27        21.30 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81       140.81        48.00        17.98        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-AA6T TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        12.36        10.62        43.59         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       16.70         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B6 
        0.92        13.68        14.07        15.32        14.37        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        4.01        12.62        27.98        23.41        17.98        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA 
       53.88        11.01         5.69        27.45        18.08        62.86 
TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.27         9.67        31.07         7.13        10.65         8.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3BM 
       30.61        15.95        26.93        33.01         6.94        21.40 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       17.75         8.94         7.73         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3QK 
       11.31        27.09        20.05        32.98        21.34        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R 
       22.72         1.51        25.02         3.45        21.24        27.68 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74         6.38        11.80        15.58        21.07        12.23 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
        3.75        12.43        22.68        76.01        67.79         3.58 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       35.24        17.82         1.64        45.04        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV 
       15.35         1.87        17.88        64.80        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAMH 
       11.90        21.04        18.90        16.27        13.74        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       71.57        91.73         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
        9.63         0.66        11.97        18.64         7.36        27.19 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4U TCGA-ZF-AA4W 
       28.41        13.41         3.48        52.73         8.61        60.16 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.43                           0.10 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                         15.50                          15.95 
[1] "0.4 - 166.0 (15.5)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1"  
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(5P15.33) MUTATED         1       62        67       60
  AMP PEAK  9(5P15.33) WILD-TYPE       3       62        60       69
D9V3, multiclass
           clus
vv          AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            62                             62
  STAGE III                           67                             60
  STAGE IV                            60                             69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK  9(5P15.33) MUTATED         55 92 25
  AMP PEAK  9(5P15.33) WILD-TYPE       66 92 28
D9V4, multiclass
          clus
vv         AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T0+T1+T2                           55                             66
  T3                                 92                             92
  T4                                 25                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  9(5P15.33) MUTATED   107  22  36   4
  AMP PEAK  9(5P15.33) WILD-TYPE 117  20  39   4
D9V5, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  N0                          107                            117
  N1                           22                             20
  N2                           36                             39
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    85   2
  AMP PEAK  9(5P15.33) WILD-TYPE 100   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     85    2
  AMP PEAK  9(5P15.33) WILD-TYPE  100    8
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           85                            100
  1                            2                              8
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    50 143
  AMP PEAK  9(5P15.33) WILD-TYPE  51 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     50  143
  AMP PEAK  9(5P15.33) WILD-TYPE   51  145
        clus
vv       AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           50                             51
  MALE                            143                            145
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5P15.33) MUTATED      15                        12   157
  AMP PEAK  9(5P15.33) WILD-TYPE    27                         9   154
D9V11, multiclass
                           clus
vv                          AMP PEAK  9(5P15.33) MUTATED
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              157
                           clus
vv                          AMP PEAK  9(5P15.33) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     5 175
  AMP PEAK  9(5P15.33) WILD-TYPE   4 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      5  175
  AMP PEAK  9(5P15.33) WILD-TYPE    4  177
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            177
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P22.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P22.3) MUTATED   110  50
  AMP PEAK 10(6P22.3) WILD-TYPE 120 103
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          160                           223 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           50                           103 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.27        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA 
       15.12        47.80         6.58         5.06         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47V 
       20.48        12.82        28.70         8.98         0.43        12.46 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 
       12.62        12.00        12.92         5.19         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       130.88       112.44        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A6AV 
       87.32        13.58         7.82        50.27        10.55        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       67.36        15.68       166.03        10.49         8.65        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       43.50        12.03        43.59        15.35         0.49        17.39 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 
        0.56        12.99         1.22        13.68        12.95        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SR 
       33.04         4.01        22.52        24.30        25.74        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC 
       22.98        27.35        19.33        58.92        62.86         6.15 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       12.36         2.27         3.06        31.07        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
        3.25         6.48        61.94        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-A42P 
       14.07        24.92         0.49        13.91         7.73        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       11.31         7.63        20.05         4.73        10.65        32.98 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       21.34        19.82         8.48         8.58        19.07        22.72 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       38.60         8.22        21.24         9.14        27.68         9.07 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       15.42         6.38        11.80        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75         3.58        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9SG 
        4.54         1.64         6.58        97.45        97.12        48.62 
TCGA-XF-A9SJ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML 
        3.22        26.27         2.24        10.82       110.60         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M 
       71.57        98.99        44.32        18.81        11.97        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.11        30.28        74.56        13.41        52.73        52.60 
TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 
       47.84        34.06        19.69        59.38        63.02        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
        8.52        47.15        19.17        10.13 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       44.94        16.83        16.77        34.98        49.12        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       19.50        14.89        14.96         5.06         8.25        16.18 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        4.67         9.96        17.56        24.26        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       23.01         0.46         0.69        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       13.08         4.90         7.20         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58        21.86        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       15.62         1.81         2.20         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        76.60        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.58        12.36         7.53        10.62        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         2.24        16.70         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       14.33         0.92        14.07        15.32        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
       16.77         8.94        12.62        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S 
       17.98        29.16         5.52        46.78        12.85        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TH 
        7.10         6.28        13.35        18.81        12.69         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK 
        9.67        10.85         7.13         8.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       26.93        35.24        33.01         7.23        20.12         6.94 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         8.94         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.36        11.31        27.09         5.62         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-H4-A2HQ 
       19.10        20.28        10.59        27.35         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A5RI 
        3.06         9.01        25.02         3.45         2.76        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX 
        1.74         1.81        21.07        13.48        14.24         1.84 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HE 
        3.75        67.79       112.83        35.24        45.04       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       15.35         1.87        17.88        64.80        79.66        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       16.27        66.64         2.10        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90        91.73         2.96         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         9.63         0.66        18.64         7.36        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RN 
       27.19        21.86        28.41         3.48        82.49        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        2.89         8.61        60.16        38.73        35.41        57.90 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                        17.16                         14.96 
[1] "0.4 - 166.0 (17.2)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.7"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(6P22.3) MUTATED         1       52        43       62
  AMP PEAK 10(6P22.3) WILD-TYPE       3       72        84       67
D10V3, multiclass
           clus
vv          AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  STAGE I                             1                             3
  STAGE II                           52                            72
  STAGE III                          43                            84
  STAGE IV                           62                            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 10(6P22.3) MUTATED         57  69  22
  AMP PEAK 10(6P22.3) WILD-TYPE       64 115  31
D10V4, multiclass
          clus
vv         AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  T0+T1+T2                          57                            64
  T3                                69                           115
  T4                                22                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 10(6P22.3) MUTATED    84  22  36   5
  AMP PEAK 10(6P22.3) WILD-TYPE 140  20  39   3
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  N0                          84                           140
  N1                          22                            20
  N2                          36                            39
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    70   4
  AMP PEAK 10(6P22.3) WILD-TYPE 115   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     70    4
  AMP PEAK 10(6P22.3) WILD-TYPE  115    6
   clus
vv  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  0                          70                           115
  1                           4                             6
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    36 124
  AMP PEAK 10(6P22.3) WILD-TYPE  65 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     36  124
  AMP PEAK 10(6P22.3) WILD-TYPE   65  164
        clus
vv       AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  FEMALE                          36                            65
  MALE                           124                           164
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P22.3) MUTATED      13                         8   133
  AMP PEAK 10(6P22.3) WILD-TYPE    29                        13   178
D10V11, multiclass
                           clus
vv                          AMP PEAK 10(6P22.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                             133
                           clus
vv                          AMP PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     6 140
  AMP PEAK 10(6P22.3) WILD-TYPE   3 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      6  140
  AMP PEAK 10(6P22.3) WILD-TYPE    3  212
                        clus
vv                       AMP PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       AMP PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           212
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q21) MUTATED    23  10
  AMP PEAK 11(6Q21) WILD-TYPE 207 143
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         33                         350 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         10                         143 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LA TCGA-CF-A47V 
       17.16        40.08         6.58        19.04        17.16        12.46 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3WX TCGA-DK-A6B5 
        7.20        21.86        18.41       130.88        10.55        41.06 
TCGA-E7-A6ME TCGA-FD-A43P TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-GC-A3BM 
       12.99        27.35        31.07        10.65        17.23        21.40 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-AATO TCGA-K4-A5RH 
       15.81        24.92        13.91         7.73        10.65         9.07 
TCGA-UY-A78K TCGA-UY-A78N TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-ZF-A9R4 
       17.62        86.83        66.64       110.60        71.57        30.28 
TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA51 
       52.60        59.38        38.73 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39        13.15        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        0.46         0.43         0.69        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       11.34        11.87        13.08        12.92         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        15.68        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
       25.74        46.78        19.79        12.85        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        4.31         9.67        10.85         7.13         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       64.44        19.46         2.24         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         0.49         8.94         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        12.43        31.56        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.73        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       6.58                        0.10 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                     130.88                      166.03 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                     19.040                      15.335 
[1] "6.6 - 130.9 (19.0)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.8"
D11V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(6Q21) MUTATED         1        9         9       14
  AMP PEAK 11(6Q21) WILD-TYPE       3      115       118      115
D11V3, multiclass
           clus
vv          AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  STAGE I                           1                           3
  STAGE II                          9                         115
  STAGE III                         9                         118
  STAGE IV                         14                         115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2  T3  T4
  AMP PEAK 11(6Q21) MUTATED         12  12   6
  AMP PEAK 11(6Q21) WILD-TYPE      109 172  47
D11V4, multiclass
          clus
vv         AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        12                         109
  T3                              12                         172
  T4                               6                          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"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 11(6Q21) MUTATED    16   4   8   1
  AMP PEAK 11(6Q21) WILD-TYPE 208  38  67   7
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        16                         208
  N1                         4                          38
  N2                         8                          67
  N3                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    17   1
  AMP PEAK 11(6Q21) WILD-TYPE 168   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     17    1
  AMP PEAK 11(6Q21) WILD-TYPE  168    9
   clus
vv  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  0                        17                         168
  1                         1                           9
[1] 2 2
[1] FALSE
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     8  25
  AMP PEAK 11(6Q21) WILD-TYPE  93 263
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      8   25
  AMP PEAK 11(6Q21) WILD-TYPE   93  263
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                         8                          93
  MALE                          25                         263
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6Q21) MUTATED       2                         3    28
  AMP PEAK 11(6Q21) WILD-TYPE    40                        18   283
D11V11, multiclass
                           clus
vv                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            28
                           clus
vv                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              40
  BLACK OR AFRICAN AMERICAN                          18
  WHITE                                             283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     1  30
  AMP PEAK 11(6Q21) WILD-TYPE   8 322
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      1   30
  AMP PEAK 11(6Q21) WILD-TYPE    8  322
                        clus
vv                       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                           8
  NOT HISPANIC OR LATINO                        30                         322
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(6Q23.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(6Q23.3) MUTATED    28  16
  AMP PEAK 12(6Q23.3) WILD-TYPE 202 137
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           44                           339 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           16                           137 
$`AMP PEAK 12(6Q23.3) MUTATED`
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A2LA TCGA-CF-A1HS TCGA-CF-A47V 
       34.98         6.58        14.89        17.16         0.43        12.46 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3IM TCGA-DK-A3WX 
        7.20         5.46        18.41       130.88         7.82        10.55 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-E7-A541 TCGA-E7-A97Q TCGA-FD-A3SS TCGA-FD-A6TD 
       30.67        15.02        17.39         8.09        12.85        12.69 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       10.65        17.23        19.46        21.40        15.81         4.50 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A40G TCGA-HQ-A2OE 
       24.92         0.49        10.65        14.27        19.07        38.60 
TCGA-K4-A5RH TCGA-UY-A78N TCGA-UY-A9PE TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T5 
        9.07        86.83         4.54        12.76        28.24        66.64 
TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAN8 TCGA-ZF-A9R4 TCGA-ZF-A9RF TCGA-ZF-A9RG 
      110.60        71.57         3.88        30.28        52.73        52.60 
TCGA-ZF-A9RN TCGA-ZF-AA4V 
       20.22        59.38 

$`AMP PEAK 12(6Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       23.01         0.46         0.69        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU 
       11.34        11.87        13.08        12.92         4.90         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       41.56        76.60        67.36        15.68        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC 
       17.62        66.02         6.94        64.44         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76         9.14        27.68        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       29.56        17.82         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      125.49        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66         3.22        66.41        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        21.11        24.13        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM 
       28.41        74.56        13.41         3.48        82.49        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                       130.88                        166.03 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                       16.485                        15.620 
[1] "0.4 - 130.9 (16.5)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(6Q23.3) MUTATED         0       10        17       15
  AMP PEAK 12(6Q23.3) WILD-TYPE       4      114       110      114
D12V3, multiclass
           clus
vv          AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           10                           114
  STAGE III                          17                           110
  STAGE IV                           15                           114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 12(6Q23.3) MUTATED         12  21   7
  AMP PEAK 12(6Q23.3) WILD-TYPE      109 163  46
D12V4, multiclass
          clus
vv         AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  T0+T1+T2                          12                           109
  T3                                21                           163
  T4                                 7                            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"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 12(6Q23.3) MUTATED    24   6   7   3
  AMP PEAK 12(6Q23.3) WILD-TYPE 200  36  68   5
D12V5, multiclass
    clus
vv   AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  N0                          24                           200
  N1                           6                            36
  N2                           7                            68
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED    22   2
  AMP PEAK 12(6Q23.3) WILD-TYPE 163   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     22    2
  AMP PEAK 12(6Q23.3) WILD-TYPE  163    8
   clus
vv  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  0                          22                           163
  1                           2                             8
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED    10  34
  AMP PEAK 12(6Q23.3) WILD-TYPE  91 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     10   34
  AMP PEAK 12(6Q23.3) WILD-TYPE   91  254
        clus
vv       AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  FEMALE                          10                            91
  MALE                            34                           254
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q23.3) MUTATED       2                         1    40
  AMP PEAK 12(6Q23.3) WILD-TYPE    40                        20   271
D12V11, multiclass
                           clus
vv                          AMP PEAK 12(6Q23.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              40
                           clus
vv                          AMP PEAK 12(6Q23.3) WILD-TYPE
  ASIAN                                                40
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED     1  40
  AMP PEAK 12(6Q23.3) WILD-TYPE   8 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED      1   40
  AMP PEAK 12(6Q23.3) WILD-TYPE    8  312
                        clus
vv                       AMP PEAK 12(6Q23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK 12(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7P21.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7P21.1) MUTATED   106  82
  AMP PEAK 13(7P21.1) WILD-TYPE 124  71
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          188                           195 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                           82                            71 
$`AMP PEAK 13(7P21.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       11.97       105.70         8.35        16.27        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       27.62         0.62        41.75        15.12        10.22        47.80 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O 
       40.08         2.66        12.39         6.58        32.84        12.16 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       12.82         9.96        28.70        24.26        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.46        13.12        12.92         4.90         5.46         5.19 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I1 
       13.58        21.86         2.14        18.41       130.88        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        50.27        23.21         9.67        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       64.18        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
      166.03        10.49        43.59        15.35         0.49        17.39 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 
       12.99         0.92         1.22        13.68         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       16.77         8.94        33.04         4.01        22.52        24.30 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        27.35        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
        3.62        26.73        11.01         5.36        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         7.10         6.28        13.35        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.27         3.06         9.67        31.07        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
        3.25         6.48        35.24        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46        21.40         2.24         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
       24.92        13.91         7.73        20.98         2.20        10.92 
TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW 
       11.31         5.62         4.73        32.98         7.00        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ 
       19.82        10.59        27.35         8.58        22.72        19.40 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.01         8.22         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K 
        6.38        15.32        13.48         1.84        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        65.75         3.58 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       35.24        29.56         4.54        97.45        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       48.62        79.66         3.22        21.04        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX 
       66.64       110.60         7.63        71.57         2.96         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 
       98.99        44.32        56.48        61.45        75.39        18.81 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       13.64        18.64        24.13        13.41        52.73        52.60 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 
        2.89        34.06        19.69        59.38        63.02         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

$`AMP PEAK 13(7P21.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       22.29        91.63       103.50        44.94        16.83        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       49.12        51.16        66.54        33.83         7.33         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       13.15        19.04        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
       14.96         4.67        17.56         8.98         1.94         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA 
       13.08         7.20        16.31         1.84        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW 
       17.72        21.30        20.81        10.55       140.81        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       76.60        41.06        13.58        12.36         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       13.97        14.33        14.07        12.95        15.32        14.37 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.62        27.98        60.66        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
        5.52        25.74        14.96        15.58        53.88        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        5.69         8.25         2.70        62.86        18.81         6.15 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.31        10.85         7.13         8.94        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        33.01         7.23        20.12         6.94 
TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81        17.75         0.49         8.94         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO 
        7.36        11.31         7.63        27.09        20.05        10.65 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HO 
       14.27        19.10        20.28         8.48        19.07         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT 
        9.14        27.68         1.74        11.80        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78P 
       12.23        16.67        14.24         3.75        31.56        67.79 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
      112.83        17.82         1.64        45.04         6.58       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
        1.87        17.88        64.80        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       23.64        28.24        18.90        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW 
       92.98        10.82        11.31        54.90        91.73         8.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        86.30        27.06         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        11.97         7.36        21.11        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.86        28.41        74.56         3.48        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       20.22         8.61        60.16        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       19.40        47.15         5.52 

  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                         0.46                          0.10 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                       16.045                        15.580 
[1] "0.5 - 166.0 (16.0)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(7P21.1) MUTATED         2       48        61       77
  AMP PEAK 13(7P21.1) WILD-TYPE       2       76        66       52
D13V3, multiclass
           clus
vv          AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           48                            76
  STAGE III                          61                            66
  STAGE IV                           77                            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 13(7P21.1) MUTATED         51 95 30
  AMP PEAK 13(7P21.1) WILD-TYPE       70 89 23
D13V4, multiclass
          clus
vv         AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  T0+T1+T2                          51                            70
  T3                                95                            89
  T4                                30                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 13(7P21.1) MUTATED    95  26  44   7
  AMP PEAK 13(7P21.1) WILD-TYPE 129  16  31   1
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  N0                          95                           129
  N1                          26                            16
  N2                          44                            31
  N3                           7                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED    82   4
  AMP PEAK 13(7P21.1) WILD-TYPE 103   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED     82    4
  AMP PEAK 13(7P21.1) WILD-TYPE  103    6
   clus
vv  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  0                          82                           103
  1                           4                             6
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED    48 142
  AMP PEAK 13(7P21.1) WILD-TYPE  53 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED     48  142
  AMP PEAK 13(7P21.1) WILD-TYPE   53  146
        clus
vv       AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  FEMALE                          48                            53
  MALE                           142                           146
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(7P21.1) MUTATED      11                        13   160
  AMP PEAK 13(7P21.1) WILD-TYPE    31                         8   151
D13V11, multiclass
                           clus
vv                          AMP PEAK 13(7P21.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             160
                           clus
vv                          AMP PEAK 13(7P21.1) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED     4 172
  AMP PEAK 13(7P21.1) WILD-TYPE   5 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED      4  172
  AMP PEAK 13(7P21.1) WILD-TYPE    5  180
                        clus
vv                       AMP PEAK 13(7P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         172
                        clus
vv                       AMP PEAK 13(7P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           180
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7P11.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(7P11.2) MUTATED   106  73
  AMP PEAK 14(7P11.2) WILD-TYPE 124  80
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          179                           204 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                           73                            80 
$`AMP PEAK 14(7P11.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 
       16.27        16.77        27.62         0.62        41.75        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ 
       10.22        47.80        33.83        40.08         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20W 
        6.58        19.04        32.84        12.16         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
        8.25        17.16        16.18        20.48        12.82        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A5U8 TCGA-CU-A0YN 
       24.26        28.41        23.01         0.43        13.12        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        4.90         5.46        13.58        21.86         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88       112.44         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20        13.58         7.82         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       23.21         9.67        48.00        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       30.67        38.24        15.02       166.03        12.36        10.49 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU 
       43.59        15.35         0.49        17.39        12.99         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
        1.22        13.68        12.95         8.09        32.02         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR 
       33.04         4.01        22.52        24.30        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       12.85        22.98        27.35        20.91         3.62        26.73 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.36        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       13.35        12.69        12.36         2.27         3.06         9.67 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY 
       10.65        17.23         3.25         6.48        35.24        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
       66.02        64.44        19.46        21.40         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 
       15.91        14.07        13.91         7.73        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ 
       10.92        11.31        20.05         5.62        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        19.82        20.28         8.48        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72        19.40        38.60         9.01         8.22 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
       21.24         9.07        11.70         1.81         6.38        15.32 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       13.48         1.84        12.43        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD 
       65.75         3.58        35.24        29.56         4.54        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SY 
       97.12        15.35        48.62        79.66         3.22        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
        2.24        66.64       110.60         7.63        71.57         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 
        6.77        98.99        56.48        61.45        75.39        18.81 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       13.64        18.64        24.13        13.41        52.73        52.60 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA5H 
        2.89        59.38        63.02        38.73        19.17 

$`AMP PEAK 14(7P11.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 
       44.94        16.83        17.16        34.98        49.12        51.16 
TCGA-4Z-AA83 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q 
       66.54         7.33         6.74        13.15        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        5.06        14.89        14.96         4.67         9.96        17.56 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94         0.46         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3QU 
       11.34        11.34        11.87        13.08         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       16.31         1.84        66.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX 
       17.62        15.62        17.72        21.30        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q 
      140.81        41.56        76.60        15.68        41.06        13.58 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        24.66         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
        0.66        14.56        13.97        14.33        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
       14.37        16.77        12.62        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y 
       17.98        29.16         5.52        25.74        14.96        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N 
       53.88        11.01        19.33         5.69         8.25         2.70 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        18.81         6.15         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        7.13         8.94        61.94        30.61        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3WC 
       33.01         7.23        20.12         6.94        15.81        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B 
       24.92         0.49         8.94         2.10         3.12         7.36 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
       11.31         7.63        27.09         4.73        10.65        14.27 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU 
       19.10        10.59         1.51         3.06        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
        2.76         9.14        27.68         1.74        15.42        11.80 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        21.07        12.23        16.67        14.24         3.75 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       31.56        17.62        37.05        67.79       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        1.64        45.04         6.58       125.49         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        66.41        12.76        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90        16.27         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ 
       10.82        11.31        54.90        91.73         8.32        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        86.30        27.06         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        11.97         7.36        21.11        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.86        28.41        74.56         3.48        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA52 
       20.22        34.06        19.69         8.61        60.16        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                        16.77                         15.50 
[1] "0.4 - 166.0 (16.8)" "0.1 - 140.8 (15.5)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(7P11.2) MUTATED         2       52        56       68
  AMP PEAK 14(7P11.2) WILD-TYPE       2       72        71       61
D14V3, multiclass
           clus
vv          AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           52                            72
  STAGE III                          56                            71
  STAGE IV                           68                            61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 14(7P11.2) MUTATED         53 88 26
  AMP PEAK 14(7P11.2) WILD-TYPE       68 96 27
D14V4, multiclass
          clus
vv         AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  T0+T1+T2                          53                            68
  T3                                88                            96
  T4                                26                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(7P11.2) MUTATED    93  20  41   7
  AMP PEAK 14(7P11.2) WILD-TYPE 131  22  34   1
D14V5, multiclass
    clus
vv   AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  N0                          93                           131
  N1                          20                            22
  N2                          41                            34
  N3                           7                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED    83   4
  AMP PEAK 14(7P11.2) WILD-TYPE 102   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED     83    4
  AMP PEAK 14(7P11.2) WILD-TYPE  102    6
   clus
vv  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  0                          83                           102
  1                           4                             6
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED    48 133
  AMP PEAK 14(7P11.2) WILD-TYPE  53 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED     48  133
  AMP PEAK 14(7P11.2) WILD-TYPE   53  155
        clus
vv       AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  FEMALE                          48                            53
  MALE                           133                           155
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7P11.2) MUTATED      12                        11   151
  AMP PEAK 14(7P11.2) WILD-TYPE    30                        10   160
D14V11, multiclass
                           clus
vv                          AMP PEAK 14(7P11.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             151
                           clus
vv                          AMP PEAK 14(7P11.2) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED     5 160
  AMP PEAK 14(7P11.2) WILD-TYPE   4 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED      5  160
  AMP PEAK 14(7P11.2) WILD-TYPE    4  192
                        clus
vv                       AMP PEAK 14(7P11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK 14(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           192
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8P11.23) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8P11.23) MUTATED    72  45
  AMP PEAK 15(8P11.23) WILD-TYPE 158 108
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           117                            266 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            45                            108 
$`AMP PEAK 15(8P11.23) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA89 
       22.29        44.94        16.83        17.16        41.75        33.83 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD 
        6.74        12.39        32.84         5.06        17.16        20.48 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A5 
       24.26        23.01         0.69         5.19        13.58         2.14 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS 
      112.44        10.59        87.32         2.20        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA71 
       23.21        10.55        17.98        30.67        38.24        13.64 
TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6ME 
       43.50        43.59        24.66         0.49        14.56        12.99 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       13.68        12.95         8.09         4.01        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U 
       17.98        46.78        19.79        12.85        27.35        20.91 
TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3ZE 
       53.88        58.92         7.10        12.69         9.67        10.65 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25         6.48        33.01        20.12        17.62        66.02 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 
       21.40         2.24        14.07        13.91         7.73         2.20 
TCGA-GD-A76B TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        7.36         7.00        14.27        21.34        19.10        10.59 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
        8.58        22.72        38.60         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A8JT 
       21.24        27.68        11.70         1.81        15.42        21.07 
TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PE 
       12.23        12.43        86.83         3.58       112.83         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG 
        1.64        45.04        97.45        97.12        15.35        48.62 
TCGA-XF-A9SH TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 
       64.80        66.64       110.60        71.57        98.99        18.81 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9RE TCGA-ZF-A9RG 
       13.64        18.64        21.11        24.13         3.48        52.60 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
        2.89        34.06         8.61        63.02        38.73        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5P 
        8.52        47.15        10.13 

$`AMP PEAK 15(8P11.23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
       16.77        34.98        27.62        49.12         0.62        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        15.12        10.22        47.80        40.08         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       28.41         8.98         1.94         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       21.86        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         7.82         8.22        21.30         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       10.49         8.65         7.53        12.03        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       38.83         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66        13.97        14.33         0.92         1.22        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO 
       12.62        22.52        27.98        23.41        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       25.74        22.98        14.96         3.62        15.58        26.73 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08         2.70         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
        6.15        12.36         2.27         3.06         4.31        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       31.07         7.13        17.23         8.94        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D 
       15.95        26.93        35.24         7.23         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46        15.81         4.50        15.91        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
        0.49         8.94         2.10         3.12        20.98        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        10.65        32.98        19.82        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS 
       27.35        19.07         1.51        19.40         3.06        25.02 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO 
        2.76         9.14         9.07         1.74         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        13.48        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
        3.75        31.56        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC 
       67.79        65.75        35.24        29.56        17.82         6.58 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
      125.49         1.87        17.88        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82        11.31        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66        11.97         7.36        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM 
       28.41        74.56        13.41        52.73        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 
       20.22        19.69        59.38        60.16        35.41        19.40 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.17         5.52 

  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                        112.83                         166.03 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                         17.98                          15.32 
[1] "0.5 - 112.8 (18.0)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(8P11.23) MUTATED         0       41        36       38
  AMP PEAK 15(8P11.23) WILD-TYPE       4       83        91       91
D15V3, multiclass
           clus
vv          AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            41                             83
  STAGE III                           36                             91
  STAGE IV                            38                             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 15(8P11.23) MUTATED         42  53  16
  AMP PEAK 15(8P11.23) WILD-TYPE       79 131  37
D15V4, multiclass
          clus
vv         AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  T0+T1+T2                           42                             79
  T3                                 53                            131
  T4                                 16                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 15(8P11.23) MUTATED    62  17  18   3
  AMP PEAK 15(8P11.23) WILD-TYPE 162  25  57   5
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  N0                           62                            162
  N1                           17                             25
  N2                           18                             57
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    52   2
  AMP PEAK 15(8P11.23) WILD-TYPE 133   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     52    2
  AMP PEAK 15(8P11.23) WILD-TYPE  133    8
   clus
vv  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  0                           52                            133
  1                            2                              8
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    30  88
  AMP PEAK 15(8P11.23) WILD-TYPE  71 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     30   88
  AMP PEAK 15(8P11.23) WILD-TYPE   71  200
        clus
vv       AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  FEMALE                           30                             71
  MALE                             88                            200
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8P11.23) MUTATED       9                         7    94
  AMP PEAK 15(8P11.23) WILD-TYPE    33                        14   217
D15V11, multiclass
                           clus
vv                          AMP PEAK 15(8P11.23) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               94
                           clus
vv                          AMP PEAK 15(8P11.23) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED     5 102
  AMP PEAK 15(8P11.23) WILD-TYPE   4 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED      5  102
  AMP PEAK 15(8P11.23) WILD-TYPE    4  250
                        clus
vv                       AMP PEAK 15(8P11.23) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       AMP PEAK 15(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            250
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8P11.21) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(8P11.21) MUTATED    87  46
  AMP PEAK 16(8P11.21) WILD-TYPE 143 107
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           133                            250 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                            46                            107 
$`AMP PEAK 16(8P11.21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       22.29        11.97       105.70        44.94        16.83        17.16 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13J TCGA-BL-A3JM 
       41.75        10.22        47.80        33.83         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
       12.39        32.84         8.35        17.16        20.48        12.82 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3QU 
       24.26        23.01         0.69        12.62        12.92         5.19 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 
       13.58        66.41        18.41       112.44        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX 
       87.32         2.20        17.72        50.27        23.21        10.55 
TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA74 
       17.98        30.67        38.24        10.49        13.64        43.50 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV 
       43.59         0.49        14.56        12.99         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SR 
       13.68        12.95         8.09        60.66        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 
       12.85        22.98        27.35        20.91        53.88        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TI TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES 
        2.70         7.10         9.67         3.25         6.48        33.01 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GD-A3OS 
       66.02        21.40         2.24         4.50         0.49        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.20         7.36         7.00        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE 
       20.28         8.48        10.59         8.58        22.72        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RI TCGA-K4-A6FZ 
        3.06         9.01        25.02         3.45        11.70         1.81 
TCGA-K4-A6MB TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78N 
       15.42        21.07        12.23        12.43        31.56        86.83 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HD 
        3.58       112.83        17.82         4.54        45.04        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-AAMG 
       97.12        15.35         1.87        48.62        64.80       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YF-AA3M 
        7.63        71.57        98.99        18.81        18.84        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
       18.64         7.36        21.11        24.13        30.28         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       52.73        52.60         2.89        19.69         8.61        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       38.73        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5P 
       10.13 

$`AMP PEAK 16(8P11.21) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S 
       91.63       103.50         8.35        16.27        16.77        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        8.25        16.18         4.67         9.96        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       28.41         8.98         1.94         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO 
       12.10        11.34        11.34        11.87        13.08         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46        16.31         1.84        21.86         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
        1.81         7.79        13.58         7.82         8.22        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67        20.81       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q 
       76.60        67.36        15.68        41.06        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 
      166.03        12.36         8.65         7.53        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
       17.39         0.56         0.66        13.97        14.33        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        22.52        27.98        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43X 
       17.98        29.16         5.52        25.74        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       15.58        26.73        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        8.25        27.45        18.08         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        20.12        17.62         6.94        64.44        19.46 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A42Q 
       13.91         7.73         2.10         3.12        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       10.65        32.98        21.34        27.35        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       19.40         8.22        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        9.07         1.74         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K 
       13.48        16.67        14.24         1.84         3.75        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        76.01        67.79        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SI 
       29.56         1.64         6.58       125.49        17.88        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        9.63         0.66        11.97        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       74.56        13.41        82.49        47.84        20.22        34.06 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA5N 
       59.38        60.16        35.41         5.52 

  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                        123.85                         166.03 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                         17.98                          15.32 
[1] "0.5 - 123.8 (18.0)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.4"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(8P11.21) MUTATED         1       43        46       41
  AMP PEAK 16(8P11.21) WILD-TYPE       3       81        81       88
D16V3, multiclass
           clus
vv          AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            43                             81
  STAGE III                           46                             81
  STAGE IV                            41                             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 16(8P11.21) MUTATED         43  62  21
  AMP PEAK 16(8P11.21) WILD-TYPE       78 122  32
D16V4, multiclass
          clus
vv         AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  T0+T1+T2                           43                             78
  T3                                 62                            122
  T4                                 21                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 16(8P11.21) MUTATED    72  17  20   5
  AMP PEAK 16(8P11.21) WILD-TYPE 152  25  55   3
D16V5, multiclass
    clus
vv   AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  N0                           72                            152
  N1                           17                             25
  N2                           20                             55
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    69   0
  AMP PEAK 16(8P11.21) WILD-TYPE 116  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     69    0
  AMP PEAK 16(8P11.21) WILD-TYPE  116   10
   clus
vv  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  0                           69                            116
  1                            0                             10
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    30 104
  AMP PEAK 16(8P11.21) WILD-TYPE  71 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     30  104
  AMP PEAK 16(8P11.21) WILD-TYPE   71  184
        clus
vv       AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           30                             71
  MALE                            104                            184
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8P11.21) MUTATED      10                         6   110
  AMP PEAK 16(8P11.21) WILD-TYPE    32                        15   201
D16V11, multiclass
                           clus
vv                          AMP PEAK 16(8P11.21) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              110
                           clus
vv                          AMP PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED     4 116
  AMP PEAK 16(8P11.21) WILD-TYPE   5 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED      4  116
  AMP PEAK 16(8P11.21) WILD-TYPE    5  236
                        clus
vv                       AMP PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            236
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(8Q22.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(8Q22.3) MUTATED   149  99
  AMP PEAK 17(8Q22.3) WILD-TYPE  81  54
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          248                           135 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                           99                            54 
$`AMP PEAK 17(8Q22.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97       103.50         8.35        16.27        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       17.16        34.98         0.62        41.75        51.16        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.39        19.04        32.84        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
        8.25        17.16        16.18        20.48        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY 
        0.43         0.69        10.95        12.62        12.00        11.34 
TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       11.87        12.92         7.20         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
       13.58        21.86         2.14        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        16.14        10.59       123.85        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX 
        7.82         8.22        17.72        50.27        23.21        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P 
       48.00        17.98        64.18        15.68        30.67        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
      166.03        10.49         8.65        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        43.59        15.35        38.83         0.49         2.24 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV 
       17.39         0.56        14.56        12.99         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 
       13.68        12.95        14.37         8.09         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ 
        4.01        27.98        60.66        24.30        25.74        46.78 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       22.98        20.91        26.73        53.88        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       13.35        12.69        12.36         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK 
       10.85        31.07         7.13        10.65         3.25        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       35.24        33.01        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        21.40         2.24         4.50        14.07        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        8.94         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       10.92        11.31         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       10.59         8.58        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14         9.07        11.70         1.81        15.42         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       14.24         1.84        12.43        31.56        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD 
       86.83        76.01        65.75         3.58       112.83        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        4.54         1.64        45.04        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV 
        1.87        48.62        64.80        79.66         3.22        12.76 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       26.27         2.24         2.10        92.98       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
       54.90         7.63        71.57         2.96         8.32        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YF-AA3M 
       44.32        61.45        75.39        18.81        18.84        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R9 
       18.64         7.36        21.11        24.13        30.28        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
       74.56         3.48        52.73        52.60        82.49        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89        19.69         8.61        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

$`AMP PEAK 17(8Q22.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       91.63       105.70        16.83        16.77        27.62        49.12 
TCGA-4Z-AA83 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
       66.54         7.33         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR 
       19.50         5.06        14.96         4.67         9.96         0.46 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.66        12.46        12.10        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1AA TCGA-DK-A1AB 
       11.34        13.08         4.90        16.31        19.00        16.70 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IT 
       17.62        15.62         1.81         7.79        13.58        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        20.81       140.81        41.56        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 
       41.06        38.24        13.58        12.36         7.53        24.66 
TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.10        16.70         0.66        13.97        14.33        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SL 
       15.32        32.02        16.77        12.62        22.52        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16         5.52        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A62N 
       14.96         3.62        15.58        19.33         8.25         2.70 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FJ-A3ZF TCGA-FJ-A871 
       62.86        18.81         6.15         2.27        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C 
        6.48        61.94        30.61        26.93         7.23         6.94 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        24.92         0.49        13.91         7.73 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GV-A3QK 
       11.31         7.63        27.09        20.05        10.65        27.35 
TCGA-GV-A40G TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-S5-AA26 
       19.07        21.24        27.68         1.74        11.80         3.75 
TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HE 
       37.05        67.79        35.24        29.56         6.58       125.49 
TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMR 
       18.90        16.27        66.64        13.74        10.82        91.73 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 
        6.77        56.48        30.94        86.30        27.06         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        9.63         0.66        11.97        27.19        21.86        13.41 
TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4V 
       47.84        34.06        59.38 

  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                         0.43                          0.10 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                       166.03                        140.81 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                       15.385                        16.270 
[1] "0.4 - 166.0 (15.4)" "0.1 - 140.8 (16.3)"
[1] "hr=" "1"  
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(8Q22.3) MUTATED         3       77        82       85
  AMP PEAK 17(8Q22.3) WILD-TYPE       1       47        45       44
D17V3, multiclass
           clus
vv          AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  STAGE I                             3                             1
  STAGE II                           77                            47
  STAGE III                          82                            45
  STAGE IV                           85                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 17(8Q22.3) MUTATED         79 116  36
  AMP PEAK 17(8Q22.3) WILD-TYPE       42  68  17
D17V4, multiclass
          clus
vv         AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  T0+T1+T2                          79                            42
  T3                               116                            68
  T4                                36                            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 17(8Q22.3) MUTATED   137  31  46   5
  AMP PEAK 17(8Q22.3) WILD-TYPE  87  11  29   3
D17V5, multiclass
    clus
vv   AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  N0                         137                            87
  N1                          31                            11
  N2                          46                            29
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED   117   6
  AMP PEAK 17(8Q22.3) WILD-TYPE  68   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED    117    6
  AMP PEAK 17(8Q22.3) WILD-TYPE   68    4
   clus
vv  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  0                         117                            68
  1                           6                             4
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED    63 187
  AMP PEAK 17(8Q22.3) WILD-TYPE  38 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED     63  187
  AMP PEAK 17(8Q22.3) WILD-TYPE   38  101
        clus
vv       AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  FEMALE                          63                            38
  MALE                           187                           101
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(8Q22.3) MUTATED      23                        12   202
  AMP PEAK 17(8Q22.3) WILD-TYPE    19                         9   109
D17V11, multiclass
                           clus
vv                          AMP PEAK 17(8Q22.3) MUTATED
  ASIAN                                              23
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             202
                           clus
vv                          AMP PEAK 17(8Q22.3) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED     5 222
  AMP PEAK 17(8Q22.3) WILD-TYPE   4 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED      5  222
  AMP PEAK 17(8Q22.3) WILD-TYPE    4  130
                        clus
vv                       AMP PEAK 17(8Q22.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         222
                        clus
vv                       AMP PEAK 17(8Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(9P24.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(9P24.1) MUTATED    54  31
  AMP PEAK 18(9P24.1) WILD-TYPE 176 122
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           85                           298 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           31                           122 
$`AMP PEAK 18(9P24.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 
       22.29        16.77        15.12        47.80         6.74         6.58 
TCGA-BT-A20V TCGA-BT-A3PJ TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AC 
        5.06        12.82         7.20         5.19         2.14       130.88 
TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-E7-A85H 
      112.44       123.85        87.32         7.82        30.67        12.95 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A43P 
       32.02        33.04         4.01        22.52        23.41        27.35 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TF 
       11.01        19.33         5.69         2.70        12.69         2.27 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IE TCGA-GC-A3BM 
        4.31        31.07        61.94        30.61        20.12        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
        2.24        15.91         0.49        13.91         7.73         2.10 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
       27.09        20.05        19.82        20.28        10.59         8.58 
TCGA-GV-A40G TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-SY-A9G0 TCGA-UY-A78K 
       19.07         8.22         1.81        15.32        12.43        17.62 
TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG 
       67.79        29.56         6.58        97.12        15.35        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMG 
       79.66         3.22        21.04        16.27        66.64       110.60 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3M TCGA-ZF-A9R0 
        7.63         2.96        27.06        75.39        13.64        18.64 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       30.28        21.86        52.73        52.60        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 
        2.89        19.69        59.38        60.16        63.02        57.90 
TCGA-ZF-AA58 
       47.15 

$`AMP PEAK 18(9P24.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 
        0.62        41.75        51.16        66.54        10.22        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66        12.39        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       13.08        12.92         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86        66.41        18.41        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20        13.58         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
        8.94        12.62        27.98        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88         5.36         8.25        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.36         3.06         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         8.94         3.25         6.48        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       64.44        19.46        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       24.92         8.94         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
       10.92        11.31        11.31         7.63         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.48        27.35        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L 
       16.67        14.24         1.84         3.75        31.56        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        86.83        76.01        65.75         3.58       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD 
       35.24        17.82         4.54         1.64        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV 
      125.49         1.87        17.88        64.80        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        28.24        26.27        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        91.73         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       56.48        30.94        61.45        86.30        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       18.84         9.63         0.66        11.97         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       24.13        27.19        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       82.49        34.06         8.61        38.73        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        19.17         5.52        10.13 

  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                       130.88                        166.03 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                        19.69                         14.99 
[1] "0.5 - 130.9 (19.7)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.3"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(9P24.1) MUTATED         0       26        31       28
  AMP PEAK 18(9P24.1) WILD-TYPE       4       98        96      101
D18V3, multiclass
           clus
vv          AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           26                            98
  STAGE III                          31                            96
  STAGE IV                           28                           101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 18(9P24.1) MUTATED         23  42  12
  AMP PEAK 18(9P24.1) WILD-TYPE       98 142  41
D18V4, multiclass
          clus
vv         AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  T0+T1+T2                          23                            98
  T3                                42                           142
  T4                                12                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 18(9P24.1) MUTATED    43   8  19   2
  AMP PEAK 18(9P24.1) WILD-TYPE 181  34  56   6
D18V5, multiclass
    clus
vv   AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  N0                          43                           181
  N1                           8                            34
  N2                          19                            56
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    33   3
  AMP PEAK 18(9P24.1) WILD-TYPE 152   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     33    3
  AMP PEAK 18(9P24.1) WILD-TYPE  152    7
   clus
vv  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  0                          33                           152
  1                           3                             7
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    20  65
  AMP PEAK 18(9P24.1) WILD-TYPE  81 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     20   65
  AMP PEAK 18(9P24.1) WILD-TYPE   81  223
        clus
vv       AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  FEMALE                          20                            81
  MALE                            65                           223
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(9P24.1) MUTATED       4                         7    71
  AMP PEAK 18(9P24.1) WILD-TYPE    38                        14   240
D18V11, multiclass
                           clus
vv                          AMP PEAK 18(9P24.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              71
                           clus
vv                          AMP PEAK 18(9P24.1) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED     3  76
  AMP PEAK 18(9P24.1) WILD-TYPE   6 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED      3   76
  AMP PEAK 18(9P24.1) WILD-TYPE    6  276
                        clus
vv                       AMP PEAK 18(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          76
                        clus
vv                       AMP PEAK 18(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           276
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(10P14) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(10P14) MUTATED    95  74
  AMP PEAK 19(10P14) WILD-TYPE 135  79
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         169                          214 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                          74                           79 
$`AMP PEAK 19(10P14) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 
       22.29        16.27        16.77        17.16        27.62         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       41.75        15.12        47.80        40.08         2.66         6.58 
TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
       32.84        19.50         5.06         5.06         8.35        16.18 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       20.48        12.82        24.26         8.98        23.01         0.43 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       12.00        11.34        12.92         5.46         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX 
       21.86         2.14        66.41       130.88       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X1 
       10.59        87.32        13.58         8.22         9.67        48.00 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       64.18        67.36        15.68        30.67        15.02       166.03 
TCGA-DK-AA6U TCGA-DK-AA74 TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
       10.49        43.50        38.83        12.99         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       12.95        14.37         8.09        32.02         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       22.52        60.66        24.30        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 
       27.35        15.58        26.73        53.88        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       58.92        12.36         2.27         3.06         9.67        31.07 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25         6.48        33.01        20.12        17.62        66.02 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       19.46         4.50        14.07         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-A767 
        7.73        20.98         2.20        10.92         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98         7.00        21.34        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48         8.58        22.72        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        9.01         8.22        25.02         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
       11.70         1.74         1.81         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       15.58        13.48        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE 
       22.68        86.83        76.01        65.75        35.24         4.54 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        97.12        15.35        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG 
        3.22        23.64        28.24         2.10        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMZ 
       11.31        54.90         7.63         2.96         6.77        44.32 
TCGA-XF-AAN4 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       27.06        13.64        18.64         7.36        24.13        30.28 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       28.41        74.56        52.73        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       19.69        59.38        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 
       19.40 

$`AMP PEAK 19(10P14) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       16.83        34.98        49.12        51.16        66.54        10.22 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       33.83         7.33         6.74        12.39        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       12.16        17.88        14.89        14.96         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 
        4.67         9.96        17.56        28.70        28.41         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.62        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 
       13.08         4.90         7.20        16.31        13.58        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00        16.70        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      123.85         2.20         7.82        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
       23.21        20.81        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
       76.60        41.06        38.24        13.58        12.36         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
        7.53        13.64        12.03        10.62        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
        0.56         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.07        15.32        16.77         4.01        12.62        27.98 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.96        20.91         3.62        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        5.69         8.25         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK 
       62.86        18.81         6.15        12.69         4.31        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13        10.65        17.23         8.94        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D 
       15.95        26.93        35.24         7.23         6.94        64.44 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40         2.24        15.81        15.91        17.75        24.92 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.10         3.12         7.36        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK 
       27.09        20.05        14.27        19.10        10.59        27.35 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
       19.07         1.51         3.45        21.24         2.76        15.42 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       21.07        12.23        16.67        14.24         1.84         3.75 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       67.79         3.58       112.83        29.56        17.82         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SL 
       45.04         6.58       125.49         1.87        17.88        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMQ TCGA-XF-AAMR 
       16.27        66.64        13.74        92.98        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32        98.99        56.48        30.94        61.45        86.30 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       11.97        21.11        27.19        21.86        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 
       52.60        82.49         2.89         8.61        60.16         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                        0.43                         0.10 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                      166.03                       140.81 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                      17.620                       14.925 
[1] "0.4 - 166.0 (17.6)" "0.1 - 140.8 (14.9)"
[1] "hr=" "1"  
D19V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(10P14) MUTATED         2       51        55       62
  AMP PEAK 19(10P14) WILD-TYPE       2       73        72       67
D19V3, multiclass
           clus
vv          AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  STAGE I                            2                            2
  STAGE II                          51                           73
  STAGE III                         55                           72
  STAGE IV                          62                           67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 19(10P14) MUTATED         52  83  24
  AMP PEAK 19(10P14) WILD-TYPE       69 101  29
D19V4, multiclass
          clus
vv         AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  T0+T1+T2                         52                           69
  T3                               83                          101
  T4                               24                           29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 19(10P14) MUTATED    84  23  34   5
  AMP PEAK 19(10P14) WILD-TYPE 140  19  41   3
D19V5, multiclass
    clus
vv   AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  N0                         84                          140
  N1                         23                           19
  N2                         34                           41
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED    79   4
  AMP PEAK 19(10P14) WILD-TYPE 106   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED     79    4
  AMP PEAK 19(10P14) WILD-TYPE  106    6
   clus
vv  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  0                         79                          106
  1                          4                            6
[1] 2 2
[1] FALSE
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED    42 130
  AMP PEAK 19(10P14) WILD-TYPE  59 158
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED     42  130
  AMP PEAK 19(10P14) WILD-TYPE   59  158
        clus
vv       AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  FEMALE                         42                           59
  MALE                          130                          158
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(10P14) MUTATED      16                         9   137
  AMP PEAK 19(10P14) WILD-TYPE    26                        12   174
D19V11, multiclass
                           clus
vv                          AMP PEAK 19(10P14) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            137
                           clus
vv                          AMP PEAK 19(10P14) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED     4 150
  AMP PEAK 19(10P14) WILD-TYPE   5 202
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED      4  150
  AMP PEAK 19(10P14) WILD-TYPE    5  202
                        clus
vv                       AMP PEAK 19(10P14) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        150
                        clus
vv                       AMP PEAK 19(10P14) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          202
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11P13) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 20(11P13) MUTATED    25  23
  AMP PEAK 20(11P13) WILD-TYPE 205 130
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          48                          335 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          23                          130 
$`AMP PEAK 20(11P13) MUTATED`
TCGA-4Z-AA7M TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-CU-A0YN 
       16.27         6.74         5.06        17.16        12.82        12.92 
TCGA-CU-A0YO TCGA-DK-A2I2 TCGA-DK-A3IV TCGA-DK-A3WX TCGA-E5-A2PC TCGA-E7-A5KE 
        4.90         7.79         9.67        10.55        43.59         0.56 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62N TCGA-FD-A62P 
       12.99         1.22        33.04        11.01         2.70         6.28 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JZ 
        9.67        31.07        15.91         7.63         5.62        19.82 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A3WS TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI 
       10.59         8.58        25.02         9.14        15.32        12.23 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9SX 
       17.62        22.68       112.83        29.56         1.64        23.64 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAN7 
       21.04         2.24       110.60        11.31         2.96        18.81 
TCGA-YF-AA3M TCGA-ZF-A9RD TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       13.64        13.41        19.69        38.73        19.17        10.13 

$`AMP PEAK 20(11P13) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.25        16.18        20.48         4.67         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.34        11.87        13.08         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        21.30        23.21        20.81       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       13.97        14.33         0.92        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        15.58        26.73        53.88        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.69         8.25        27.45        18.08        58.92         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         3.06         4.31        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81         4.50        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       14.27        21.34        19.10        20.28         8.48        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        9.01         8.22         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       11.80        15.58        21.07        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N 
        1.84         3.75        12.43        31.56        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD 
       76.01        67.79        65.75         3.58        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        4.54        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 
        3.22        66.41        12.76        11.90        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
       10.82        54.90         7.63        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       34.06         8.61        59.38        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15         5.52 

  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                      112.83                       166.03 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                       12.87                        16.27 
[1] "0.6 - 112.8 (12.9)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.6"
D20V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 20(11P13) MUTATED         0       13        12       23
  AMP PEAK 20(11P13) WILD-TYPE       4      111       115      106
D20V3, multiclass
           clus
vv          AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  STAGE I                            0                            4
  STAGE II                          13                          111
  STAGE III                         12                          115
  STAGE IV                          23                          106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 20(11P13) MUTATED         14  23   8
  AMP PEAK 20(11P13) WILD-TYPE      107 161  45
D20V4, multiclass
          clus
vv         AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  T0+T1+T2                         14                          107
  T3                               23                          161
  T4                                8                           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"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 20(11P13) MUTATED    19   5  15   4
  AMP PEAK 20(11P13) WILD-TYPE 205  37  60   4
D20V5, multiclass
    clus
vv   AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  N0                         19                          205
  N1                          5                           37
  N2                         15                           60
  N3                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED    15   0
  AMP PEAK 20(11P13) WILD-TYPE 170  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED     15    0
  AMP PEAK 20(11P13) WILD-TYPE  170   10
   clus
vv  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  0                         15                          170
  1                          0                           10
[1] 2 2
[1] FALSE
D20V7, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED    14  34
  AMP PEAK 20(11P13) WILD-TYPE  87 254
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED     14   34
  AMP PEAK 20(11P13) WILD-TYPE   87  254
        clus
vv       AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  FEMALE                         14                           87
  MALE                           34                          254
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11P13) MUTATED       4                         1    42
  AMP PEAK 20(11P13) WILD-TYPE    38                        20   269
D20V11, multiclass
                           clus
vv                          AMP PEAK 20(11P13) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             42
                           clus
vv                          AMP PEAK 20(11P13) WILD-TYPE
  ASIAN                                               38
  BLACK OR AFRICAN AMERICAN                           20
  WHITE                                              269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED     2  45
  AMP PEAK 20(11P13) WILD-TYPE   7 307
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED      2   45
  AMP PEAK 20(11P13) WILD-TYPE    7  307
                        clus
vv                       AMP PEAK 20(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         45
                        clus
vv                       AMP PEAK 20(11P13) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          307
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(11Q13.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(11Q13.3) MUTATED    73  55
  AMP PEAK 21(11Q13.3) WILD-TYPE 157  98
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           128                            255 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                            55                             98 
$`AMP PEAK 21(11Q13.3) MUTATED`
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A2LA 
       16.83        34.98         0.62         2.66        32.84        17.16 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82        17.56        28.70        24.26        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN 
       23.01         0.43        12.46        11.34        11.34        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         7.20         5.46         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL 
       66.41        17.62        10.59         7.79        87.32        13.58 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        7.82        17.72        10.55        48.00        17.98        64.18 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       30.67        15.02        43.50        12.03        10.62        43.59 
TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B5 
       38.83         0.56         0.66         1.22         8.09         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43P 
       33.04         4.01        60.66        24.30        22.98        27.35 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A62N 
       20.91        15.58        26.73        11.01         5.36         2.70 
TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-A3IB 
       13.35         3.06         9.67        31.07        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12        66.02        64.44        19.46        21.40         2.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 
       15.91        14.07         8.94         7.73        20.98         2.20 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63         5.62         4.73         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB 
       19.07        19.40        38.60         9.01        21.24         2.76 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        9.14        15.32        21.07        12.23        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD 
        3.75        12.43        22.68        76.01         3.58       112.83 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T4 
       29.56         1.64        97.12        12.76        21.04        16.27 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
        2.10        11.31         7.63        71.57         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YF-AA3M TCGA-ZF-A9R7 
        6.77        44.32        27.06         3.88        13.64        21.86 
TCGA-ZF-AA51 TCGA-ZF-AA53 
       38.73        57.90 

$`AMP PEAK 21(11Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.27        44.94        16.77        17.16        27.62        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       33.83        40.08         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
       20.48         9.96         8.98         1.94         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       13.58        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IN 
       16.14        15.62         1.81       123.85         2.20         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        20.81       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       41.56        76.60        67.36        15.68        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       13.64        15.35        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       16.70        17.39        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        0.92        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
       32.02        16.77        12.62        22.52        27.98        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX 
       12.85        14.96         3.62        53.88        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       35.24        17.62         6.94        15.81         4.50        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B 
       24.92         0.49        13.91         2.10         3.12         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO 
       10.92        11.31        11.31        27.09        20.05        10.65 
TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
       32.98        19.10        22.72         1.51         3.06         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       25.02         3.45        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        15.42         6.38        11.80        15.58        13.48 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P 
       16.67        31.56        17.62        37.05        86.83        67.79 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC 
       65.75        35.24        17.82         4.54        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45       125.49        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66         3.22        66.41        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 
       28.24        26.27        18.90         2.24        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY 
       92.98        10.82       110.60        54.90        91.73        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        86.30        75.39        18.81 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        30.28        27.19        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        63.02        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                          0.43                           0.10 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                        112.83                         166.03 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                        14.155                         16.270 
[1] "0.4 - 112.8 (14.2)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.3"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 21(11Q13.3) MUTATED         0       46        35       46
  AMP PEAK 21(11Q13.3) WILD-TYPE       4       78        92       83
D21V3, multiclass
           clus
vv          AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            46                             78
  STAGE III                           35                             92
  STAGE IV                            46                             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 21(11Q13.3) MUTATED         45  54  19
  AMP PEAK 21(11Q13.3) WILD-TYPE       76 130  34
D21V4, multiclass
          clus
vv         AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  T0+T1+T2                           45                             76
  T3                                 54                            130
  T4                                 19                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 21(11Q13.3) MUTATED    71  14  27   5
  AMP PEAK 21(11Q13.3) WILD-TYPE 153  28  48   3
D21V5, multiclass
    clus
vv   AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  N0                           71                            153
  N1                           14                             28
  N2                           27                             48
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED    56   2
  AMP PEAK 21(11Q13.3) WILD-TYPE 129   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED     56    2
  AMP PEAK 21(11Q13.3) WILD-TYPE  129    8
   clus
vv  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  0                           56                            129
  1                            2                              8
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED    40  89
  AMP PEAK 21(11Q13.3) WILD-TYPE  61 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED     40   89
  AMP PEAK 21(11Q13.3) WILD-TYPE   61  199
        clus
vv       AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  FEMALE                           40                             61
  MALE                             89                            199
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(11Q13.3) MUTATED      10                        11   102
  AMP PEAK 21(11Q13.3) WILD-TYPE    32                        10   209
D21V11, multiclass
                           clus
vv                          AMP PEAK 21(11Q13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              102
                           clus
vv                          AMP PEAK 21(11Q13.3) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED     2 119
  AMP PEAK 21(11Q13.3) WILD-TYPE   7 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED      2  119
  AMP PEAK 21(11Q13.3) WILD-TYPE    7  233
                        clus
vv                       AMP PEAK 21(11Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       AMP PEAK 21(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(11Q22.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(11Q22.2) MUTATED    46  23
  AMP PEAK 22(11Q22.2) WILD-TYPE 184 130
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            69                            314 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            23                            130 
$`AMP PEAK 22(11Q22.2) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42E 
       22.29         0.62        15.12         8.35        12.82        24.26 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 
        1.94        23.01        11.34         7.20         1.84        21.86 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       10.59        87.32        13.58        10.55        48.00        17.98 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV TCGA-E7-A97Q 
       12.03        10.62        43.59         0.66         1.22         8.09 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ 
       33.04        60.66        27.35        26.73        11.01        27.45 
TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3B TCGA-G2-AA3D 
       58.92         3.06         9.67        31.07        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GD-A6C6 
       19.46         2.24        15.91        24.92        20.98         2.20 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AB 
        7.63         5.62        20.28        10.59         8.58         2.76 
TCGA-K4-A4AC TCGA-K4-A6MB TCGA-LC-A66R TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-SY-A9G0 
        9.14        15.42        15.32        12.23         1.84        12.43 
TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A9SY 
       22.68         3.58        29.56         1.64        97.12        21.04 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMX TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RF 
        2.10        11.31         6.77        13.64        21.86        52.73 
TCGA-ZF-AA51 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       38.73        19.17        10.13 

$`AMP PEAK 22(11Q22.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       49.12        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       17.16        16.18        20.48         4.67         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.70        28.41         8.98         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90         5.46         5.19        16.31        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85         2.20         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV 
       21.30        23.21         9.67        20.81       140.81        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E5-A4U1 
        8.65         7.53        13.64        43.50        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.56        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       13.68        14.07        12.95        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94         4.01        12.62        22.52        27.98 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        15.58        53.88        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       21.40        15.81         4.50        14.07        17.75         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B 
        8.94        13.91         7.73         2.10         3.12         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 
       10.92        11.31        11.31        27.09        20.05         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       19.82         8.48        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        3.45        21.24        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.81         6.38        11.80        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       16.67        14.24         3.75        31.56        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       86.83        76.01        67.79        65.75       112.83        35.24 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         4.54        45.04         6.58        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
        3.22        66.41        12.76        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82       110.60        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        7.36        21.11        24.13        30.28        27.19        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        63.02        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N 
       47.15         5.52 

  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                          0.62                           0.10 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                         97.12                         166.03 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                        13.580                         16.225 
[1] "0.6 - 97.1 (13.6)"  "0.1 - 166.0 (16.2)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 22(11Q22.2) MUTATED         0       23        16       30
  AMP PEAK 22(11Q22.2) WILD-TYPE       4      101       111       99
D22V3, multiclass
           clus
vv          AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            23                            101
  STAGE III                           16                            111
  STAGE IV                            30                             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 22(11Q22.2) MUTATED         24  30  11
  AMP PEAK 22(11Q22.2) WILD-TYPE       97 154  42
D22V4, multiclass
          clus
vv         AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  T0+T1+T2                           24                             97
  T3                                 30                            154
  T4                                 11                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 22(11Q22.2) MUTATED    32  11  17   3
  AMP PEAK 22(11Q22.2) WILD-TYPE 192  31  58   5
D22V5, multiclass
    clus
vv   AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  N0                           32                            192
  N1                           11                             31
  N2                           17                             58
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED    32   1
  AMP PEAK 22(11Q22.2) WILD-TYPE 153   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED     32    1
  AMP PEAK 22(11Q22.2) WILD-TYPE  153    9
   clus
vv  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  0                           32                            153
  1                            1                              9
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED    19  50
  AMP PEAK 22(11Q22.2) WILD-TYPE  82 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED     19   50
  AMP PEAK 22(11Q22.2) WILD-TYPE   82  238
        clus
vv       AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  FEMALE                           19                             82
  MALE                             50                            238
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(11Q22.2) MUTATED       3                         2    61
  AMP PEAK 22(11Q22.2) WILD-TYPE    39                        19   250
D22V11, multiclass
                           clus
vv                          AMP PEAK 22(11Q22.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               61
                           clus
vv                          AMP PEAK 22(11Q22.2) WILD-TYPE
  ASIAN                                                 39
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED     1  64
  AMP PEAK 22(11Q22.2) WILD-TYPE   8 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED      1   64
  AMP PEAK 22(11Q22.2) WILD-TYPE    8  288
                        clus
vv                       AMP PEAK 22(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 22(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(12P12.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(12P12.1) MUTATED    80  42
  AMP PEAK 23(12P12.1) WILD-TYPE 150 111
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           122                            261 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            42                            111 
$`AMP PEAK 23(12P12.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       22.29        27.62        41.75        15.12        10.22        47.80 
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20R 
       40.08         6.74        19.04        32.84        17.88         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06         8.25        16.18        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN 
       24.26         1.94        12.00        11.34        11.34        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IM 
        4.90         7.20         5.46        66.41        18.41         7.82 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       50.27        10.55        48.00        64.18        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       30.67        15.02       166.03        12.36        10.49         7.53 
TCGA-DK-AA71 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 
       13.64         0.49         0.56        12.99        32.02        33.04 
TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX 
       60.66        12.85        27.35        53.88         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FJ-A3Z7 
       27.45         6.28        13.35        18.81         2.27        31.07 
TCGA-FJ-A3Z9 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
        7.13         6.48        35.24        17.62        66.02        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A762 
       21.40         2.24        15.81        14.07        13.91         7.63 
TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       20.05         7.00        19.82         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        19.07        38.60         3.06         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A83P 
        3.45        21.24         9.14         9.07        11.70         6.38 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78O 
       15.32        13.48        12.23        31.56        17.62        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A9SI TCGA-XF-A9SV 
       67.79         3.58        35.24        29.56        79.66        12.76 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 
        7.63         2.96         6.77        98.99        44.32        86.30 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       75.39        18.81        13.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       30.28        13.41         2.89        59.38        60.16        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 
       57.90        19.40 

$`AMP PEAK 23(12P12.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J 
        0.62        51.16        66.54        33.83         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T 
       12.39         6.58        13.15        12.16        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
       14.96         8.35        17.16         4.67        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       13.12        12.10        11.87        13.08         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84        13.58        21.86         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        17.72        21.30        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L 
      140.81        17.98        41.56        76.60        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.58         8.65        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
       17.39         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        19.79        22.98        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY 
        3.62        15.58        26.73        11.01        19.33         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC 
       18.08        58.92         2.70         7.10        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69        12.36         3.06         4.31         9.67        10.85 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        33.01         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       64.44         4.50        15.91        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 
        7.36        10.92        11.31        11.31        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98        14.27        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB 
       20.28        22.72         1.51        19.40        25.02         2.76 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 
       27.68         1.74         1.81        15.42        11.80        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        16.67        14.24         1.84         3.75        12.43 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD 
       37.05        22.68        86.83        65.75       112.83        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        4.54         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73         8.32        56.48        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       18.64        27.19        21.86        28.41        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 
       19.69         8.61        63.02        35.41         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                         15.22                          15.95 
[1] "0.5 - 166.0 (15.2)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 23(12P12.1) MUTATED         3       47        38       36
  AMP PEAK 23(12P12.1) WILD-TYPE       1       77        89       93
D23V3, multiclass
           clus
vv          AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  STAGE I                              3                              1
  STAGE II                            47                             77
  STAGE III                           38                             89
  STAGE IV                            36                             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 23(12P12.1) MUTATED         45  56  14
  AMP PEAK 23(12P12.1) WILD-TYPE       76 128  39
D23V4, multiclass
          clus
vv         AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  T0+T1+T2                           45                             76
  T3                                 56                            128
  T4                                 14                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 23(12P12.1) MUTATED    74  15  19   3
  AMP PEAK 23(12P12.1) WILD-TYPE 150  27  56   5
D23V5, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  N0                           74                            150
  N1                           15                             27
  N2                           19                             56
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED    64   3
  AMP PEAK 23(12P12.1) WILD-TYPE 121   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED     64    3
  AMP PEAK 23(12P12.1) WILD-TYPE  121    7
   clus
vv  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  0                           64                            121
  1                            3                              7
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED    34  91
  AMP PEAK 23(12P12.1) WILD-TYPE  67 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED     34   91
  AMP PEAK 23(12P12.1) WILD-TYPE   67  197
        clus
vv       AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  FEMALE                           34                             67
  MALE                             91                            197
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(12P12.1) MUTATED      12                         7    99
  AMP PEAK 23(12P12.1) WILD-TYPE    30                        14   212
D23V11, multiclass
                           clus
vv                          AMP PEAK 23(12P12.1) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               99
                           clus
vv                          AMP PEAK 23(12P12.1) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED     2 111
  AMP PEAK 23(12P12.1) WILD-TYPE   7 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED      2  111
  AMP PEAK 23(12P12.1) WILD-TYPE    7  241
                        clus
vv                       AMP PEAK 23(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       AMP PEAK 23(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            241
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(12Q15) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(12Q15) MUTATED    68  42
  AMP PEAK 24(12Q15) WILD-TYPE 162 111
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         110                          273 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          42                          111 
$`AMP PEAK 24(12Q15) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97         8.35         0.62        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V 
        6.74         6.58        19.04        17.88         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
        8.25        16.18         9.96        28.70        24.26        23.01 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        12.10        11.34        11.34         4.90         7.20 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        1.84        21.86         2.14        66.41        18.41       130.88 
TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6P 
      123.85        10.55        64.18        67.36        15.68        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 
      166.03        12.36        10.49         7.53        13.64        12.03 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
       17.39         0.56        12.99        13.68        12.95         8.09 
TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S 
       15.58         5.69        27.45        58.92         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF 
       18.81         6.15         3.06        31.07         6.48        61.94 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
       15.95        35.24        17.62        64.44        21.40         2.24 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
       14.07        13.91        11.31        21.34         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.35         8.58         1.51        19.40        38.60         3.06 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A83P TCGA-MV-A51V TCGA-S5-A6DX 
        3.45        21.24        11.70         6.38        13.48         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PE TCGA-XF-A9SH TCGA-XF-A9SI 
       12.43        31.56        76.01         4.54        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
        3.22        12.76        11.90         2.96         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-YF-AA3M 
       44.32        61.45        86.30        27.06        18.81        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RN TCGA-ZF-AA4U 
        7.36        21.11        30.28        74.56        20.22         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA53 
       59.38        57.90 

$`AMP PEAK 24(12Q15) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       91.63       103.50       105.70        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.77        17.16        34.98        27.62        49.12        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        7.33        12.39        13.15        32.84        12.16        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35        17.16        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR 
       12.82        17.56        28.41         8.98         1.94         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.62        12.26        13.12        11.87        13.08        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
        5.46         5.19        16.31        13.58        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        17.98        41.56        76.60        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 
       30.67        38.24        13.58         8.65        43.50        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        0.92         1.22        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N 
       11.01        19.33         5.36         8.25        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        7.10        62.86        12.69        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25        30.61        26.93        33.01         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       66.02         6.94        19.46        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         0.49         8.94         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB 
       19.07        22.72         9.01         8.22        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68         9.07         1.74         1.81        15.42 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       14.24         3.75        17.62        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       67.79        65.75         3.58       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SL 
       97.12        15.35         1.87        17.88        48.62        66.41 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        8.32        56.48        30.94        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        9.63         0.66        11.97        18.64        24.13        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4W 
       82.49        47.84         2.89        34.06        19.69        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                      166.03                       140.81 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                       13.64                        16.67 
[1] "0.6 - 166.0 (13.6)" "0.1 - 140.8 (16.7)"
[1] "hr=" "1"  
D24V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 24(12Q15) MUTATED         2       38        37       36
  AMP PEAK 24(12Q15) WILD-TYPE       2       86        90       93
D24V3, multiclass
           clus
vv          AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  STAGE I                            2                            2
  STAGE II                          38                           86
  STAGE III                         37                           90
  STAGE IV                          36                           93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 24(12Q15) MUTATED         34  49  19
  AMP PEAK 24(12Q15) WILD-TYPE       87 135  34
D24V4, multiclass
          clus
vv         AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  T0+T1+T2                         34                           87
  T3                               49                          135
  T4                               19                           34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 24(12Q15) MUTATED    66  11  23   1
  AMP PEAK 24(12Q15) WILD-TYPE 158  31  52   7
D24V5, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  N0                         66                          158
  N1                         11                           31
  N2                         23                           52
  N3                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED    63   2
  AMP PEAK 24(12Q15) WILD-TYPE 122   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED     63    2
  AMP PEAK 24(12Q15) WILD-TYPE  122    8
   clus
vv  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  0                         63                          122
  1                          2                            8
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED    33  81
  AMP PEAK 24(12Q15) WILD-TYPE  68 207
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED     33   81
  AMP PEAK 24(12Q15) WILD-TYPE   68  207
        clus
vv       AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  FEMALE                         33                           68
  MALE                           81                          207
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(12Q15) MUTATED      16                         5    89
  AMP PEAK 24(12Q15) WILD-TYPE    26                        16   222
D24V11, multiclass
                           clus
vv                          AMP PEAK 24(12Q15) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             89
                           clus
vv                          AMP PEAK 24(12Q15) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED     2 106
  AMP PEAK 24(12Q15) WILD-TYPE   7 246
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED      2  106
  AMP PEAK 24(12Q15) WILD-TYPE    7  246
                        clus
vv                       AMP PEAK 24(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        106
                        clus
vv                       AMP PEAK 24(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          246
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(13Q22.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(13Q22.1) MUTATED    76  43
  AMP PEAK 25(13Q22.1) WILD-TYPE 154 110
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           119                            264 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                            43                            110 
$`AMP PEAK 25(13Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-4Z-AA87 
       22.29       105.70        16.83        16.77        41.75        47.80 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20U 
        6.74         6.58        19.04        32.84        19.50        14.96 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A8HX 
       20.48        12.82         1.94         0.46         0.43        11.34 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IK 
       12.92         7.20        16.31         1.81        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
       13.58        17.72        50.27        21.30        23.21        48.00 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       67.36        15.68        41.06        38.24        15.02       166.03 
TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A7DU 
       10.49        13.64        12.03        43.59        17.39         0.92 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SM TCGA-FD-A43X 
        8.09         8.94        33.04        22.52        17.98         3.62 
TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       11.01         7.10         6.15        12.36         3.06         4.31 
TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3B TCGA-G2-AA3D 
       10.65         6.48        61.94        15.95        66.02        64.44 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OP 
       15.81         4.50        15.91        17.75         0.49         2.10 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX 
       20.98        10.92        11.31        10.65         7.00        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5ND 
       19.82        20.28         8.48        27.35        19.40         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A6MB 
        8.22         3.45        21.24         9.14         9.07        15.42 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K 
       11.80        15.32        13.48        14.24        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        86.83        67.79        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       29.56        17.82         6.58        97.45        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ 
       48.62        26.27         2.10        10.82         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 
       91.73         6.77        98.99        56.48        61.45        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
        7.36        21.11        63.02         8.52        19.17 

$`AMP PEAK 25(13Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        91.63       103.50         8.35        16.27        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
       17.16        34.98        27.62        49.12         0.62        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        15.12        10.22        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
        2.66        12.39        13.15        12.16        17.88         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        13.08         4.90         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN 
       15.62        10.59         7.79       123.85         7.82         8.22 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
       41.56        76.60        30.67        13.58        12.36         8.65 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
        7.53        43.50        10.62        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37        32.02        16.77 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        27.98        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       18.81        12.69         2.27         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
        7.13        17.23         8.94         3.25        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       19.46        21.40         2.24        14.07        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
       13.91         7.73         3.12         2.20         7.36        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
        7.63        27.09        20.05         5.62         4.73        32.98 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       14.27        21.34        10.59         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R 
        1.51        38.60         3.06        25.02         2.76        27.68 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
       11.70         1.74         1.81         6.38        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M 
       12.23        16.67         1.84         3.75        12.43        22.68 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE 
       76.01       112.83         4.54         1.64        45.04       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
        2.24        16.27        66.64        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 
       11.31        54.90         2.96         8.32        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        9.63         0.66        11.97        13.64        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        60.16        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        57.90        19.40        47.15         5.52        10.13 

  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                          0.43                           0.10 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                        15.950                         15.465 
[1] "0.4 - 166.0 (15.9)" "0.1 - 140.8 (15.5)"
[1] "hr=" "1.2"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 25(13Q22.1) MUTATED         1       34        41       42
  AMP PEAK 25(13Q22.1) WILD-TYPE       3       90        86       87
D25V3, multiclass
           clus
vv          AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            34                             90
  STAGE III                           41                             86
  STAGE IV                            42                             87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 25(13Q22.1) MUTATED         33  59  18
  AMP PEAK 25(13Q22.1) WILD-TYPE       88 125  35
D25V4, multiclass
          clus
vv         AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  T0+T1+T2                           33                             88
  T3                                 59                            125
  T4                                 18                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 25(13Q22.1) MUTATED    72  15  24   4
  AMP PEAK 25(13Q22.1) WILD-TYPE 152  27  51   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  N0                           72                            152
  N1                           15                             27
  N2                           24                             51
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED    60   3
  AMP PEAK 25(13Q22.1) WILD-TYPE 125   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED     60    3
  AMP PEAK 25(13Q22.1) WILD-TYPE  125    7
   clus
vv  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  0                           60                            125
  1                            3                              7
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED    25  96
  AMP PEAK 25(13Q22.1) WILD-TYPE  76 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED     25   96
  AMP PEAK 25(13Q22.1) WILD-TYPE   76  192
        clus
vv       AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  FEMALE                           25                             76
  MALE                             96                            192
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(13Q22.1) MUTATED       6                         6   104
  AMP PEAK 25(13Q22.1) WILD-TYPE    36                        15   207
D25V11, multiclass
                           clus
vv                          AMP PEAK 25(13Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              104
                           clus
vv                          AMP PEAK 25(13Q22.1) WILD-TYPE
  ASIAN                                                 36
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED     3 110
  AMP PEAK 25(13Q22.1) WILD-TYPE   6 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED      3  110
  AMP PEAK 25(13Q22.1) WILD-TYPE    6  242
                        clus
vv                       AMP PEAK 25(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       AMP PEAK 25(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            242
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(16P13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(16P13.2) MUTATED    47  35
  AMP PEAK 26(16P13.2) WILD-TYPE 183 118
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            82                            301 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            35                            118 
$`AMP PEAK 26(16P13.2) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-BT-A0S7 TCGA-BT-A20V 
        8.35        16.27        17.16         0.62         6.58         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU 
        8.25        17.16         8.98        12.62         7.20         5.19 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV 
        7.79        13.58         7.82         8.22        50.27         9.67 
TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       48.00        67.36       166.03        10.49         7.53        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97Q 
       43.59        15.35         0.49        12.99        12.95         8.09 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A5BY TCGA-FD-A6TD 
       60.66        24.30        19.79        20.91         8.25        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO 
        2.27         3.06         9.67        10.65         3.25        35.24 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GD-A76B 
       20.12        17.62        66.02        21.40         2.24         7.36 
TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-H4-A2HQ 
       10.92         5.62        32.98        14.27        19.82        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P 
       38.60         3.06         9.01         3.45         2.76         6.38 
TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A9PD TCGA-XF-A9SJ 
       15.32        14.24         1.84        31.56        17.82         3.22 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML 
       28.24        26.27        66.64         2.10       110.60         7.63 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9RD 
       91.73         6.77        44.32        18.81        18.64        13.41 
TCGA-ZF-A9RF TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       52.73        19.69        59.38        60.16 

$`AMP PEAK 26(16P13.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50       105.70        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        16.77        34.98        27.62        49.12        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         5.46        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
      123.85        87.32         2.20        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       13.58        12.36         8.65        13.64        43.50        10.62 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        24.66         0.10         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
        0.56         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        1.22        13.68        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       46.78        12.85        22.98        27.35        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81         6.15        12.36 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85        31.07         7.13        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        6.48        61.94        30.61        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
        7.23         6.94        64.44        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 
       11.31        11.31         7.63        27.09        20.05         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         7.00        21.34        19.10        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        8.22        25.02        21.24         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 
       11.70         1.74         1.81        15.42        11.80        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        13.48        12.23        16.67         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       17.62        37.05        22.68        86.83        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       65.75         3.58       112.83        35.24        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.64        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 
       66.41        12.76        11.90        23.64        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        16.27        13.74        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 
       54.90        71.57         2.96         8.32        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       74.56         3.48        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        34.06         8.61        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                         13.20                          16.27 
[1] "0.5 - 166.0 (13.2)" "0.1 - 140.8 (16.3)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 26(16P13.2) MUTATED         1       18        28       34
  AMP PEAK 26(16P13.2) WILD-TYPE       3      106        99       95
D26V3, multiclass
           clus
vv          AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            18                            106
  STAGE III                           28                             99
  STAGE IV                            34                             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 26(16P13.2) MUTATED         19  35  20
  AMP PEAK 26(16P13.2) WILD-TYPE      102 149  33
D26V4, multiclass
          clus
vv         AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  T0+T1+T2                           19                            102
  T3                                 35                            149
  T4                                 20                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 26(16P13.2) MUTATED    41  10  19   4
  AMP PEAK 26(16P13.2) WILD-TYPE 183  32  56   4
D26V5, multiclass
    clus
vv   AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  N0                           41                            183
  N1                           10                             32
  N2                           19                             56
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED    36   4
  AMP PEAK 26(16P13.2) WILD-TYPE 149   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED     36    4
  AMP PEAK 26(16P13.2) WILD-TYPE  149    6
   clus
vv  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  0                           36                            149
  1                            4                              6
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED    21  61
  AMP PEAK 26(16P13.2) WILD-TYPE  80 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED     21   61
  AMP PEAK 26(16P13.2) WILD-TYPE   80  227
        clus
vv       AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  FEMALE                           21                             80
  MALE                             61                            227
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(16P13.2) MUTATED       5                         4    69
  AMP PEAK 26(16P13.2) WILD-TYPE    37                        17   242
D26V11, multiclass
                           clus
vv                          AMP PEAK 26(16P13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               69
                           clus
vv                          AMP PEAK 26(16P13.2) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED     1  74
  AMP PEAK 26(16P13.2) WILD-TYPE   8 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED      1   74
  AMP PEAK 26(16P13.2) WILD-TYPE    8  278
                        clus
vv                       AMP PEAK 26(16P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       AMP PEAK 26(16P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            278
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(16Q22.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(16Q22.1) MUTATED    59  44
  AMP PEAK 27(16Q22.1) WILD-TYPE 171 109
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           103                            280 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            44                            109 
$`AMP PEAK 27(16Q22.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-BL-A13J 
       11.97       105.70         8.35         0.62        47.80         2.66 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        6.58        32.84         5.06         5.06         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47X 
       12.82        28.70        24.26         8.98         0.43        12.62 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS 
        5.46         2.14         7.79        13.58         7.82        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S 
        9.67        48.00        64.18        15.68        38.24       166.03 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q 
        7.53        43.59        38.83         1.22        13.68         8.09 
TCGA-FD-A3B3 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT 
       32.02        24.30        23.41        27.35        15.58        11.01 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S 
        5.36         8.25        27.45        18.08         6.28        13.35 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE 
        6.15         2.27         3.06         9.67        10.85        10.65 
TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
        3.25        35.24        33.01        17.62        66.02        64.44 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       21.40         2.24        24.92         0.49         8.94         7.73 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW 
       20.98         7.36         7.63        10.65        32.98        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX 
        2.76        15.42        11.80        15.32        14.24         1.84 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PE TCGA-XF-A9SG 
       31.56        22.68        65.75       112.83         4.54        48.62 
TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
        2.24        71.57        91.73         6.77        98.99        44.32 
TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA54 
       18.64        21.86        74.56        13.41        60.16        19.40 
TCGA-ZF-AA5H 
       19.17 

$`AMP PEAK 27(16Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        91.63       103.50        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.77        17.16        34.98        27.62        49.12        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 
       51.16        66.54        15.12        10.22        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74        12.39        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB 
       17.88        19.50        14.89        14.96         8.35        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 
       20.48         4.67         9.96        17.56        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        2.20         8.22        17.72        21.30        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        17.98        41.56        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       41.06        30.67        15.02        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
        8.65        13.64        43.50        12.03        10.62        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 
        0.92        14.07        12.95        15.32        14.37        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        22.98        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N 
       26.73        53.88        19.33         5.69        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        7.10        62.86        18.81        12.69        12.36         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF 
       31.07         7.13        17.23         8.94         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       30.61        15.95        26.93         7.23        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       13.91         2.10         3.12         2.20        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31        27.09        20.05         5.62         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
       27.35         8.58        19.07        22.72         1.51        38.60 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81         6.38        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       16.67         3.75        12.43        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       76.01        67.79         3.58        35.24        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.64        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       15.35         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96         8.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        13.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       30.28        27.19        28.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        63.02        38.73        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15         5.52        10.13 

  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                          0.43                           0.10 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                        13.680                         16.225 
[1] "0.4 - 166.0 (13.7)" "0.1 - 140.8 (16.2)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 27(16Q22.1) MUTATED         0       24        39       38
  AMP PEAK 27(16Q22.1) WILD-TYPE       4      100        88       91
D27V3, multiclass
           clus
vv          AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            24                            100
  STAGE III                           39                             88
  STAGE IV                            38                             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 27(16Q22.1) MUTATED         22  54  19
  AMP PEAK 27(16Q22.1) WILD-TYPE       99 130  34
D27V4, multiclass
          clus
vv         AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  T0+T1+T2                           22                             99
  T3                                 54                            130
  T4                                 19                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 27(16Q22.1) MUTATED    55  11  23   5
  AMP PEAK 27(16Q22.1) WILD-TYPE 169  31  52   3
D27V5, multiclass
    clus
vv   AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  N0                           55                            169
  N1                           11                             31
  N2                           23                             52
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    42   5
  AMP PEAK 27(16Q22.1) WILD-TYPE 143   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     42    5
  AMP PEAK 27(16Q22.1) WILD-TYPE  143    5
   clus
vv  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  0                           42                            143
  1                            5                              5
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    35  68
  AMP PEAK 27(16Q22.1) WILD-TYPE  66 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     35   68
  AMP PEAK 27(16Q22.1) WILD-TYPE   66  220
        clus
vv       AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  FEMALE                           35                             66
  MALE                             68                            220
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(16Q22.1) MUTATED       6                         7    83
  AMP PEAK 27(16Q22.1) WILD-TYPE    36                        14   228
D27V11, multiclass
                           clus
vv                          AMP PEAK 27(16Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               83
                           clus
vv                          AMP PEAK 27(16Q22.1) WILD-TYPE
  ASIAN                                                 36
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED     2  94
  AMP PEAK 27(16Q22.1) WILD-TYPE   7 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED      2   94
  AMP PEAK 27(16Q22.1) WILD-TYPE    7  258
                        clus
vv                       AMP PEAK 27(16Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 27(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(17Q12) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 28(17Q12) MUTATED    88  67
  AMP PEAK 28(17Q12) WILD-TYPE 142  86
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         155                          228 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          67                           86 
$`AMP PEAK 28(17Q12) MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 
       11.97        17.16        34.98         0.62        41.75        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       10.22        47.80        40.08         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
        6.58        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35         8.25        20.48         9.96        28.70         8.98 
TCGA-CF-A1HR TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 
        0.46        12.62        11.34         7.20        16.31         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        2.14        66.41        18.41       112.44        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 
       87.32         7.82        50.27        48.00        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 
       30.67        15.02       166.03        10.49         7.53        13.64 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       43.59        15.35         0.49        17.39         0.56        14.56 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.99        13.68        12.95         8.94        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43U 
       60.66        24.30        25.74        46.78        27.35        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA 
        3.62        26.73         5.36        58.92         7.10        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         2.27         4.31 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       31.07         3.25        20.12        66.02        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
       21.40         0.49         2.10         7.36        10.92        11.31 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ 
        4.73        10.65        32.98         7.00        14.27        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-MV-A51V 
        3.45        21.24        11.70         1.81        11.80        13.48 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78N TCGA-UY-A78O 
       12.23        14.24         1.84        31.56        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF 
       65.75         3.58       112.83         6.58        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9T0 
       15.35         1.87        17.88        48.62         3.22        26.27 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 
        8.32        56.48        86.30        11.97        13.64        30.28 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4T 
       28.41        74.56        13.41        47.84        20.22        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       59.38        63.02        35.41         8.52        19.17 

$`AMP PEAK 28(17Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       44.94        16.83        16.77        27.62        49.12        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
       66.54        33.83         7.33        13.15        19.04        32.84 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06        17.16        16.18         4.67        12.82 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
       17.56        24.26        28.41         1.94        23.01         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 
       12.92         4.90         5.46         5.19        13.58        21.86 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
        1.81       123.85         2.20        13.58         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        41.56        76.60        15.68        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       13.58        12.36         8.65        43.50        12.03        10.62 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83        24.66         0.10         2.24        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 
       13.97        14.33         0.92         1.22        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37         8.09        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR 
       27.98        23.41        17.98        29.16         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        22.98        14.96        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       19.33         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.28        13.35         3.06         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        35.24        33.01         7.23        17.62 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75        24.92         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       20.98         2.20        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB 
        5.62        21.34        19.10        22.72        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14        27.68         9.07         1.74        15.42         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 
       15.32        15.58        21.07        16.67         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        22.68        67.79        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9SH 
       17.82         4.54         1.64        45.04       125.49        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAMY 
       13.74        92.98        10.82        54.90         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       44.32        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.11        24.13        27.19        21.86         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W 
       52.60        82.49         2.89        34.06         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       38.73        57.90        19.40        47.15         5.52        10.13 

  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                        0.46                         0.10 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                      166.03                       140.81 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                      14.560                       16.225 
[1] "0.5 - 166.0 (14.6)" "0.1 - 140.8 (16.2)"
[1] "hr=" "1.1"
D28V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 28(17Q12) MUTATED         2       47        48       60
  AMP PEAK 28(17Q12) WILD-TYPE       2       77        79       69
D28V3, multiclass
           clus
vv          AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  STAGE I                            2                            2
  STAGE II                          47                           77
  STAGE III                         48                           79
  STAGE IV                          60                           69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 28(17Q12) MUTATED         52  70  28
  AMP PEAK 28(17Q12) WILD-TYPE       69 114  25
D28V4, multiclass
          clus
vv         AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  T0+T1+T2                         52                           69
  T3                               70                          114
  T4                               28                           25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 28(17Q12) MUTATED    87  16  40   2
  AMP PEAK 28(17Q12) WILD-TYPE 137  26  35   6
D28V5, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  N0                         87                          137
  N1                         16                           26
  N2                         40                           35
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED    71   4
  AMP PEAK 28(17Q12) WILD-TYPE 114   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     71    4
  AMP PEAK 28(17Q12) WILD-TYPE  114    6
   clus
vv  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  0                         71                          114
  1                          4                            6
[1] 2 2
[1] FALSE
D28V7, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED    39 120
  AMP PEAK 28(17Q12) WILD-TYPE  62 168
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     39  120
  AMP PEAK 28(17Q12) WILD-TYPE   62  168
        clus
vv       AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  FEMALE                         39                           62
  MALE                          120                          168
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(17Q12) MUTATED      14                         9   128
  AMP PEAK 28(17Q12) WILD-TYPE    28                        12   183
D28V11, multiclass
                           clus
vv                          AMP PEAK 28(17Q12) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            128
                           clus
vv                          AMP PEAK 28(17Q12) WILD-TYPE
  ASIAN                                               28
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED     6 139
  AMP PEAK 28(17Q12) WILD-TYPE   3 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED      6  139
  AMP PEAK 28(17Q12) WILD-TYPE    3  213
                        clus
vv                       AMP PEAK 28(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        139
                        clus
vv                       AMP PEAK 28(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          213
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(17Q23.3) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(17Q23.3) MUTATED   105  76
  AMP PEAK 29(17Q23.3) WILD-TYPE 125  77
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           181                            202 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                            76                             77 
$`AMP PEAK 29(17Q23.3) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
      103.50        16.27        16.77         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       15.12        47.80        40.08         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       20.48        28.70         8.98         0.46         0.43         0.69 
TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       12.62        11.34        12.92        16.31         1.84        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       18.41       112.44        16.14        10.59         7.79        87.32 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
        7.82        17.72        50.27        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       64.18        67.36        30.67        15.02       166.03        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ 
        8.65         7.53        13.64        12.03        43.59         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B4 
       17.39         0.56        14.56        12.99        13.68        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP 
        8.94        33.04         4.01        60.66        24.30        25.74 
TCGA-FD-A3SQ TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       46.78        20.91         3.62        26.73         5.36        27.45 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TF 
       58.92         7.10        62.86        18.81        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        3.06         4.31         9.67        31.07        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3D 
        3.25         6.48        30.61        35.24        17.62        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B 
       19.46        21.40         7.73         2.10         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       10.92        11.31        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        19.82        20.28         8.48        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.07        19.40        38.60         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
       21.24         9.07        11.70         1.81        15.42        11.80 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 
       15.32        13.48        12.23        14.24         1.84        31.56 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        65.75         3.58 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       17.82         4.54         6.58        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SY TCGA-XF-A9T0 
        1.87        17.88        48.62         3.22        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.24         2.10        13.74        10.82       110.60        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       56.48        86.30        11.97        13.64        24.13        30.28 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN 
       28.41        74.56        13.41         3.48        52.73        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 
       34.06        19.69        59.38        63.02        35.41         8.52 
TCGA-ZF-AA5H 
       19.17 

$`AMP PEAK 29(17Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       22.29        11.97        91.63       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 
       16.83        17.16        34.98        27.62        49.12        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A2LB 
       10.22        33.83         7.33        13.15        19.04        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        1.94        23.01        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E 
       13.08         4.90         7.20         5.46         5.19        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AF 
       21.86         2.14        19.00        16.70       130.88        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
       15.62         1.81       123.85         2.20        13.58         8.22 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW 
       21.30        23.21         9.67        20.81       140.81        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T 
       76.60        15.68        41.06        38.24        13.58        12.36 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
        2.24        16.70         0.66        13.97        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
       32.02        12.62        22.52        27.98        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       29.16         5.52        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        15.58        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
        8.25        18.08         2.70         6.28        13.35         6.15 
TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EK 
       12.69        10.85         7.13         8.94        61.94        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        33.01         7.23        20.12        66.02         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         0.49         8.94        13.91         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.10        10.59        22.72         1.51         3.06        25.02 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 
        2.76         9.14        27.68         1.74         6.38        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78P 
       21.07        16.67         3.75        12.43        17.62        67.79 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE 
      112.83        35.24        29.56         1.64        45.04       125.49 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66        66.41        12.76        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ 
       28.24        18.90        16.27        66.64        92.98        54.90 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        61.45        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       18.81         3.88        18.84         9.63         0.66        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RL 
        7.36        21.11        27.19        21.86        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 
       47.84         2.89         8.61        60.16        38.73        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40        47.15         5.52        10.13 

  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                          0.43                           0.10 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                         15.32                          15.93 
[1] "0.4 - 166.0 (15.3)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1.1"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 29(17Q23.3) MUTATED         2       49        58       73
  AMP PEAK 29(17Q23.3) WILD-TYPE       2       75        69       56
D29V3, multiclass
           clus
vv          AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            49                             75
  STAGE III                           58                             69
  STAGE IV                            73                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 29(17Q23.3) MUTATED         53 90 28
  AMP PEAK 29(17Q23.3) WILD-TYPE       68 94 25
D29V4, multiclass
          clus
vv         AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  T0+T1+T2                           53                             68
  T3                                 90                             94
  T4                                 28                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 29(17Q23.3) MUTATED    95  22  46   4
  AMP PEAK 29(17Q23.3) WILD-TYPE 129  20  29   4
D29V5, multiclass
    clus
vv   AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  N0                           95                            129
  N1                           22                             20
  N2                           46                             29
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED    83   5
  AMP PEAK 29(17Q23.3) WILD-TYPE 102   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED     83    5
  AMP PEAK 29(17Q23.3) WILD-TYPE  102    5
   clus
vv  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  0                           83                            102
  1                            5                              5
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED    52 134
  AMP PEAK 29(17Q23.3) WILD-TYPE  49 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED     52  134
  AMP PEAK 29(17Q23.3) WILD-TYPE   49  154
        clus
vv       AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  FEMALE                           52                             49
  MALE                            134                            154
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(17Q23.3) MUTATED      18                         8   151
  AMP PEAK 29(17Q23.3) WILD-TYPE    24                        13   160
D29V11, multiclass
                           clus
vv                          AMP PEAK 29(17Q23.3) MUTATED
  ASIAN                                               18
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              151
                           clus
vv                          AMP PEAK 29(17Q23.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED     6 165
  AMP PEAK 29(17Q23.3) WILD-TYPE   3 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED      6  165
  AMP PEAK 29(17Q23.3) WILD-TYPE    3  187
                        clus
vv                       AMP PEAK 29(17Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          165
                        clus
vv                       AMP PEAK 29(17Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            187
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(19Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 30(19Q12) MUTATED    98  53
  AMP PEAK 30(19Q12) WILD-TYPE 132 100
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         151                          232 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          53                          100 
$`AMP PEAK 30(19Q12) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.27        16.77         0.62        41.75        51.16        15.12 
TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V 
       47.80         6.74        19.04        32.84        12.16         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C 
        8.35         8.25        17.16        16.18        20.48        28.70 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X 
       24.26         1.94        23.01         0.46         0.43        12.62 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 
       12.00        11.34        12.92         5.46        16.31        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I4 
       66.41        18.41        16.70       112.44         1.81       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       87.32        13.58        48.00        64.18        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       30.67        38.24        15.02       166.03        10.49         8.65 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE 
       12.03        43.59        15.35        38.83         0.49         0.56 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B8 
       12.99         0.92        13.68        12.95        32.02        12.62 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       24.30        23.41        19.79        12.85        22.98        27.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       20.91         3.62         8.25        27.45        18.08         6.28 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       18.81         3.06         4.31        10.85        31.07        17.23 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25        61.94        35.24        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
       64.44        19.46         4.50        15.91        14.07        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP 
       13.91         7.73         7.36        11.31         4.73        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        19.40        38.60         9.01         8.22        25.02 
TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-MV-A51V 
        2.76         9.07         1.74        15.42        11.80        13.48 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC 
       14.24         1.84        31.56        37.05        65.75         3.58 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
       35.24        29.56         6.58        97.12        15.35        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMQ 
        3.22        12.76        21.04        28.24         2.24        71.57 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 
        6.77        98.99        44.32        56.48        86.30        75.39 
TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RF TCGA-ZF-A9RL 
       18.81         9.63        13.64        21.11        52.73        82.49 
TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       20.22        19.69        59.38        38.73        19.40         8.52 
TCGA-ZF-AA58 
       47.15 

$`AMP PEAK 30(19Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.39         6.58        13.15        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       14.89        14.96         4.67        12.82         9.96        17.56 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       28.41         8.98         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.10        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E 
       13.08         4.90         7.20         5.19         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        2.14        19.00       130.88        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       10.59         7.79         2.20         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6Q 
      140.81        17.98        41.56        76.60        41.06        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 
       12.36         7.53        13.64        43.50        10.62        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70        17.39         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       13.97        14.33         1.22        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        8.09        16.77         8.94        33.04         4.01        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        60.66        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        14.96        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         5.36         5.69        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       13.35        62.86         6.15        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EJ 
        9.67         7.13        10.65         8.94         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM 
       15.95        26.93        33.01         7.23         6.94        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
        2.24        15.81        17.75         0.49         8.94         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 
        3.12        20.98         2.20        10.92        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QI 
       27.09        20.05         5.62        10.65        19.10        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WU 
       27.35         8.58        22.72         1.51         3.06         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P 
       21.24         9.14        27.68        11.70         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        21.07        12.23        16.67         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       12.43        17.62        22.68        86.83        76.01        67.79 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD 
      112.83        17.82         4.54         1.64        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
      125.49         1.87        17.88        48.62        64.80        66.41 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        23.64        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 
       54.90         7.63        91.73         2.96         8.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       61.45        27.06         3.88        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RM 
       28.41        74.56        13.41         3.48        52.60        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
        2.89        34.06         8.61        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.17         5.52        10.13 

  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                        0.43                         0.10 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                      166.03                       140.81 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                      17.230                       14.725 
[1] "0.4 - 166.0 (17.2)" "0.1 - 140.8 (14.7)"
[1] "hr=" "1.4"
D30V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 30(19Q12) MUTATED         1       42        50       56
  AMP PEAK 30(19Q12) WILD-TYPE       3       82        77       73
D30V3, multiclass
           clus
vv          AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  STAGE I                            1                            3
  STAGE II                          42                           82
  STAGE III                         50                           77
  STAGE IV                          56                           73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 30(19Q12) MUTATED         40  78  22
  AMP PEAK 30(19Q12) WILD-TYPE       81 106  31
D30V4, multiclass
          clus
vv         AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  T0+T1+T2                         40                           81
  T3                               78                          106
  T4                               22                           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 30(19Q12) MUTATED    80  18  37   2
  AMP PEAK 30(19Q12) WILD-TYPE 144  24  38   6
D30V5, multiclass
    clus
vv   AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  N0                         80                          144
  N1                         18                           24
  N2                         37                           38
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED    73   4
  AMP PEAK 30(19Q12) WILD-TYPE 112   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED     73    4
  AMP PEAK 30(19Q12) WILD-TYPE  112    6
   clus
vv  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  0                         73                          112
  1                          4                            6
[1] 2 2
[1] FALSE
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED    36 117
  AMP PEAK 30(19Q12) WILD-TYPE  65 171
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED     36  117
  AMP PEAK 30(19Q12) WILD-TYPE   65  171
        clus
vv       AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  FEMALE                         36                           65
  MALE                          117                          171
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(19Q12) MUTATED      16                         7   122
  AMP PEAK 30(19Q12) WILD-TYPE    26                        14   189
D30V11, multiclass
                           clus
vv                          AMP PEAK 30(19Q12) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                            122
                           clus
vv                          AMP PEAK 30(19Q12) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED     3 135
  AMP PEAK 30(19Q12) WILD-TYPE   6 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED      3  135
  AMP PEAK 30(19Q12) WILD-TYPE    6  217
                        clus
vv                       AMP PEAK 30(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        135
                        clus
vv                       AMP PEAK 30(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          217
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(19Q13.43) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 31(19Q13.43) MUTATED    93  52
  AMP PEAK 31(19Q13.43) WILD-TYPE 137 101
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            145                             238 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                             52                             101 
$`AMP PEAK 31(19Q13.43) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.27        16.77         0.62        41.75        51.16        15.12 
TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X 
       47.80         6.74        19.04        32.84         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
       16.18        20.48        12.82        28.70        24.26         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CF-A5UA 
        1.94        23.01         0.46         0.43        12.62        12.00 
TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.34         7.20         5.46        16.31        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IK 
       18.41        16.70       130.88       112.44       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       13.58         7.82         9.67        17.98        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 
       15.68        38.24        15.02       166.03        10.49        13.64 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       12.03        43.59        15.35         0.49        17.39         0.56 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 
       12.99         0.92         1.22        12.95         8.09        32.02 
TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X 
        8.94        23.41        12.85        22.98        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A6TB TCGA-FD-A6TF 
       15.58        11.01         8.25        27.45        18.81         2.27 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        4.31        10.85        31.07        17.23         3.25        61.94 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
       35.24        20.12        66.02        15.91        14.07        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R 
       13.91         7.73         3.12        20.98         7.36        11.31 
TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ 
       19.82        20.28         8.48        10.59        19.07        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-AAQO TCGA-S5-A6DX 
       38.60         9.01         2.76        15.42        11.80         1.84 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
        3.75        17.62        37.05        65.75         3.58        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
       29.56        17.82        45.04        97.12        15.35        79.66 
TCGA-XF-A9SX TCGA-XF-A9T3 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY 
       23.64         2.24       110.60        71.57         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H 
       44.32        56.48        86.30        75.39        18.81        18.84 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RL TCGA-ZF-A9RN 
        9.63        21.11        30.28        21.86        82.49        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       34.06        19.69        59.38        38.73        19.40         8.52 
TCGA-ZF-AA58 
       47.15 

$`AMP PEAK 31(19Q13.43) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH 
        5.06        14.89        14.96         8.35        17.16         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        9.96        17.56        28.41         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.46        12.10        12.26        13.12        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 
       11.87        13.08        12.92         4.90         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       13.58         2.14        19.00        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
        1.81        10.59         7.79        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q 
       48.00        41.56        76.60        41.06        30.67        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 
       12.36         8.65         7.53        43.50        10.62        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         2.24        16.70         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       13.97        14.33        13.68        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        27.35        14.96        26.73        53.88 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       19.33         5.36         5.69        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       12.36         3.06         9.67         7.13        10.65         8.94 
TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
        6.48        30.61        15.95        26.93        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
       15.81         4.50        17.75         0.49         8.94         2.10 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20        10.92        11.31         7.63        27.09         5.62 
TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.73        19.10        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        3.06         8.22        25.02         3.45        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       27.68         9.07        11.70         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       14.24        12.43        31.56        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD 
       67.79       112.83         4.54         1.64         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
      125.49         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82        11.31        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A9TC 
        8.32        30.94        61.45        27.06         3.88         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       11.97        13.64        18.64         7.36        24.13        27.19 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       47.84         2.89         8.61        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.17         5.52        10.13 

  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                           0.43                            0.10 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                         166.03                          140.81 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                         17.390                          14.465 
[1] "0.4 - 166.0 (17.4)" "0.1 - 140.8 (14.5)"
[1] "hr=" "1.3"
D31V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 31(19Q13.43) MUTATED         1       40        47       55
  AMP PEAK 31(19Q13.43) WILD-TYPE       3       84        80       74
D31V3, multiclass
           clus
vv          AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  STAGE I                               1                               3
  STAGE II                             40                              84
  STAGE III                            47                              80
  STAGE IV                             55                              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  AMP PEAK 31(19Q13.43) MUTATED         36  70  25
  AMP PEAK 31(19Q13.43) WILD-TYPE       85 114  28
D31V4, multiclass
          clus
vv         AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  T0+T1+T2                            36                              85
  T3                                  70                             114
  T4                                  25                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 31(19Q13.43) MUTATED    74  20  32   5
  AMP PEAK 31(19Q13.43) WILD-TYPE 150  22  43   3
D31V5, multiclass
    clus
vv   AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  N0                            74                             150
  N1                            20                              22
  N2                            32                              43
  N3                             5                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED    66   5
  AMP PEAK 31(19Q13.43) WILD-TYPE 119   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED     66    5
  AMP PEAK 31(19Q13.43) WILD-TYPE  119    5
   clus
vv  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  0                            66                             119
  1                             5                               5
[1] 2 2
[1] FALSE
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED    41 106
  AMP PEAK 31(19Q13.43) WILD-TYPE  60 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED     41  106
  AMP PEAK 31(19Q13.43) WILD-TYPE   60  182
        clus
vv       AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  FEMALE                            41                              60
  MALE                             106                             182
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(19Q13.43) MUTATED      13                         8   119
  AMP PEAK 31(19Q13.43) WILD-TYPE    29                        13   192
D31V11, multiclass
                           clus
vv                          AMP PEAK 31(19Q13.43) MUTATED
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               119
                           clus
vv                          AMP PEAK 31(19Q13.43) WILD-TYPE
  ASIAN                                                  29
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED     3 128
  AMP PEAK 31(19Q13.43) WILD-TYPE   6 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED      3  128
  AMP PEAK 31(19Q13.43) WILD-TYPE    6  224
                        clus
vv                       AMP PEAK 31(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           128
                        clus
vv                       AMP PEAK 31(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             224
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(20Q11.21) MUTATION ANALYSIS
D32V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 32(20Q11.21) MUTATED   147  96
  AMP PEAK 32(20Q11.21) WILD-TYPE  83  57
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            243                             140 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                             96                              57 
$`AMP PEAK 32(20Q11.21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97       103.50       105.70        16.27        44.94 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       10.22        47.80        40.08         6.74         6.58        19.04 
TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
       32.84        17.88        19.50         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
        8.35         8.25        20.48         9.96        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN 
       10.95        12.66        12.62        11.34        11.34        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90         7.20         5.46         1.84         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       130.88       112.44         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 
       17.72        50.27        23.21         9.67        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        64.18        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       38.24        15.02       166.03        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       13.64        43.50        43.59        15.35        38.83         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
       17.39         0.56        12.99         1.22        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.09        32.02        33.04         4.01        22.52        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        23.41        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ 
       22.98        27.35         3.62        26.73        11.01        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         7.10        13.35        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69        12.36         2.27         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       31.07        10.65         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       15.95        35.24        17.62        66.02        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 
       20.98         2.20         7.36        11.31        11.31        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
       19.10        19.82        20.28         8.48        10.59         8.58 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        19.40        38.60         3.06         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
        3.45        21.24         9.14         9.07        11.70         1.81 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX 
       11.80        15.58        13.48        12.23        16.67         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       76.01        65.75         3.58        35.24        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        1.64        45.04        97.45        97.12        15.35         1.87 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
       79.66         3.22        12.76        23.64        21.04         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ 
       16.27        66.64         2.10        10.82         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       91.73         2.96         6.77        98.99        44.32        30.94 
TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       18.84        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RG 
       30.28        21.86        28.41        74.56        13.41        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       82.49        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        63.02        38.73        35.41        19.40        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

$`AMP PEAK 32(20Q11.21) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7Y 
       91.63         8.35        16.83        16.77        17.16        49.12 
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX 
       15.12        33.83         7.33         2.66        12.39        13.15 
TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       12.16        14.96        17.16        16.18         4.67        12.82 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       17.56         0.69        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.87        13.08         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58        21.86        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       15.62        21.30        20.81       140.81        41.56        76.60 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.58        12.36        12.03        10.62        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.92        14.07        15.32        14.37        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S 
       12.62        27.98        17.98        29.16         5.52        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       20.91        15.58        53.88        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3Z9 
        8.25         2.70         6.28        62.86         3.06         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       17.23         8.94        26.93        33.01         7.23        20.12 
TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 
        6.94        17.75         3.12        10.92         7.63        27.09 
TCGA-GU-A767 TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-K4-A4AB 
        4.73        27.35        22.72         1.51         9.01         2.76 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
       27.68         1.74        15.42         6.38        15.32        21.07 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HC 
       14.24         3.75        67.79       112.83        17.82         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW 
      125.49        17.88        48.62        64.80        66.41        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
       28.24        26.27        18.90        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
       11.31        54.90         8.32        56.48        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4W 
       11.97        27.19         3.48        52.73        34.06        60.16 
TCGA-ZF-AA53 TCGA-ZF-AA56 
       57.90         8.52 

  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                           0.43                            0.10 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                         166.03                          140.81 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                          16.27                           15.22 
[1] "0.4 - 166.0 (16.3)" "0.1 - 140.8 (15.2)"
[1] "hr=" "1.1"
D32V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 32(20Q11.21) MUTATED         2       77        77       87
  AMP PEAK 32(20Q11.21) WILD-TYPE       2       47        50       42
D32V3, multiclass
           clus
vv          AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  STAGE I                               2                               2
  STAGE II                             77                              47
  STAGE III                            77                              50
  STAGE IV                             87                              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  AMP PEAK 32(20Q11.21) MUTATED         75 117  33
  AMP PEAK 32(20Q11.21) WILD-TYPE       46  67  20
D32V4, multiclass
          clus
vv         AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  T0+T1+T2                            75                              46
  T3                                 117                              67
  T4                                  33                              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 32(20Q11.21) MUTATED   132  27  53   7
  AMP PEAK 32(20Q11.21) WILD-TYPE  92  15  22   1
D32V5, multiclass
    clus
vv   AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  N0                           132                              92
  N1                            27                              15
  N2                            53                              22
  N3                             7                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED   114   7
  AMP PEAK 32(20Q11.21) WILD-TYPE  71   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED    114    7
  AMP PEAK 32(20Q11.21) WILD-TYPE   71    3
   clus
vv  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  0                           114                              71
  1                             7                               3
[1] 2 2
[1] FALSE
D32V7, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED    69 178
  AMP PEAK 32(20Q11.21) WILD-TYPE  32 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED     69  178
  AMP PEAK 32(20Q11.21) WILD-TYPE   32  110
        clus
vv       AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  FEMALE                            69                              32
  MALE                             178                             110
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(20Q11.21) MUTATED      19                        12   204
  AMP PEAK 32(20Q11.21) WILD-TYPE    23                         9   107
D32V11, multiclass
                           clus
vv                          AMP PEAK 32(20Q11.21) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               204
                           clus
vv                          AMP PEAK 32(20Q11.21) WILD-TYPE
  ASIAN                                                  23
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                 107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED     4 222
  AMP PEAK 32(20Q11.21) WILD-TYPE   5 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED      4  222
  AMP PEAK 32(20Q11.21) WILD-TYPE    5  130
                        clus
vv                       AMP PEAK 32(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           222
                        clus
vv                       AMP PEAK 32(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             130
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(22Q12.2) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 33(22Q12.2) MUTATED    52  27
  AMP PEAK 33(22Q12.2) WILD-TYPE 178 126
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            79                            304 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            27                            126 
$`AMP PEAK 33(22Q12.2) MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA86 TCGA-4Z-AA87 
      103.50         8.35        44.94        34.98        10.22        47.80 
TCGA-BL-A0C8 TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-C4-A0F6 TCGA-CF-A8HY 
       40.08         8.35        16.18        12.82        23.01        11.34 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS 
       66.41        18.41       112.44        87.32         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       23.21        10.55        38.24        15.02       166.03        10.49 
TCGA-DK-AA77 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A85H TCGA-FD-A3B6 
       10.62         0.49        17.39         0.56        12.95        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BV 
        4.01        23.41        29.16        27.35        11.01         5.36 
TCGA-FD-A62O TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3D 
        7.10        61.94        35.24        33.01        66.02        64.44 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A764 
       21.40         2.24        14.07         0.49         7.73        20.05 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        4.73        14.27        19.82         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-LT-A5Z6 TCGA-S5-A6DX TCGA-SY-A9G0 
        8.58        19.07        38.60        15.58         1.84        12.43 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI 
       37.05        76.01       112.83         4.54        48.62        79.66 
TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       26.27         2.10       110.60         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9RF 
        8.32         6.77        98.99        18.64        30.28        52.73 
TCGA-ZF-AA4R 
       34.06 

$`AMP PEAK 33(22Q12.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7O 
       22.29        11.97        91.63       105.70        16.27        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.77        17.16        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J 
       51.16        66.54        15.12        33.83         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        5.06         8.25        17.16        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         7.82        17.72        21.30         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T 
       67.36        15.68        41.06        30.67        13.58        12.36 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC 
        8.65         7.53        13.64        43.50        12.03        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        24.30        17.98         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        22.98        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        19.33         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08        58.92         2.70         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       15.95        26.93         7.23        20.12        17.62         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46        15.81         4.50        15.91        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62        10.65        32.98         7.00        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
       20.28        22.72         1.51        19.40         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       16.67        14.24         3.75        31.56        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        67.79        65.75         3.58        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SJ 
       97.12        15.35         1.87        17.88        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN0 
       10.82        11.31        54.90         2.96        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                        166.03                         140.81 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                        19.820                         15.335 
[1] "0.5 - 166.0 (19.8)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.6"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 33(22Q12.2) MUTATED         2       28        29       19
  AMP PEAK 33(22Q12.2) WILD-TYPE       2       96        98      110
D33V3, multiclass
           clus
vv          AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            28                             96
  STAGE III                           29                             98
  STAGE IV                            19                            110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 33(22Q12.2) MUTATED         28  36   9
  AMP PEAK 33(22Q12.2) WILD-TYPE       93 148  44
D33V4, multiclass
          clus
vv         AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  T0+T1+T2                           28                             93
  T3                                 36                            148
  T4                                  9                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 33(22Q12.2) MUTATED    51   8  11   2
  AMP PEAK 33(22Q12.2) WILD-TYPE 173  34  64   6
D33V5, multiclass
    clus
vv   AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  N0                           51                            173
  N1                            8                             34
  N2                           11                             64
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED    41   1
  AMP PEAK 33(22Q12.2) WILD-TYPE 144   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED     41    1
  AMP PEAK 33(22Q12.2) WILD-TYPE  144    9
   clus
vv  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  0                           41                            144
  1                            1                              9
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED    20  60
  AMP PEAK 33(22Q12.2) WILD-TYPE  81 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED     20   60
  AMP PEAK 33(22Q12.2) WILD-TYPE   81  228
        clus
vv       AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  FEMALE                           20                             81
  MALE                             60                            228
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(22Q12.2) MUTATED       6                         7    63
  AMP PEAK 33(22Q12.2) WILD-TYPE    36                        14   248
D33V11, multiclass
                           clus
vv                          AMP PEAK 33(22Q12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               63
                           clus
vv                          AMP PEAK 33(22Q12.2) WILD-TYPE
  ASIAN                                                 36
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED     3  68
  AMP PEAK 33(22Q12.2) WILD-TYPE   6 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED      3   68
  AMP PEAK 33(22Q12.2) WILD-TYPE    6  284
                        clus
vv                       AMP PEAK 33(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       AMP PEAK 33(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            284
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    46  37
  DEL PEAK  1(1P36.11) WILD-TYPE 184 116
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            83                            300 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            37                            116 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 
       22.29         8.35        16.77        17.16        34.98         0.62 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20W 
       15.12        10.22         6.58        19.04        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       20.48         9.96        17.56        24.26         0.46         0.43 
TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       12.62         7.20         5.46         1.84        18.41        16.14 
TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A6B6 TCGA-DK-AA6Q 
        7.79        17.72        21.30        10.55        30.67        13.58 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A3B5 
       10.49         7.53        43.50        12.03        43.59         8.94 
TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TG 
        5.52        15.58        19.33        58.92        12.36         3.06 
TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GU-A763 TCGA-GU-A764 
       10.65        26.93        64.44        19.46        27.09        20.05 
TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF 
        5.62        32.98        14.27        10.59        22.72         3.06 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 
       25.02        21.24         9.14         1.74        15.42        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD 
       13.48        12.23        22.68        76.01        65.75       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SV 
       29.56        17.82        97.12        15.35         3.22        12.76 
TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN5 
       23.64       110.60         6.77        30.94        61.45        75.39 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA54 
       24.13        30.28        82.49        57.90        19.40 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        27.62        49.12        41.75        51.16        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39        13.15        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        12.82        28.70        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        13.08        12.92         4.90         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86         2.14        66.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        23.21         9.67        20.81       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W 
       41.06        38.24        15.02       166.03        12.36         8.65 
TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69         2.27         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        15.95        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        4.50        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         7.00        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
       20.28         8.48        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
       19.40        38.60         9.01         8.22         3.45         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO 
       27.68         9.07        11.70         1.81         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.32        21.07        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P 
       12.43        31.56        17.62        37.05        86.83        67.79 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
        3.58        35.24         4.54         1.64        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        66.41        11.90        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        52.60        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41         8.52        47.15        19.17         5.52        10.13 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        112.83                         166.03 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        16.770                         15.485 
[1] "0.4 - 112.8 (16.8)" "0.1 - 166.0 (15.5)"
[1] "hr=" "1.1"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.11) MUTATED         1       26        28       28
  DEL PEAK  1(1P36.11) WILD-TYPE       3       98        99      101
D34V3, multiclass
           clus
vv          DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            26                             98
  STAGE III                           28                             99
  STAGE IV                            28                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED         25  43   9
  DEL PEAK  1(1P36.11) WILD-TYPE       96 141  44
D34V4, multiclass
          clus
vv         DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1+T2                           25                             96
  T3                                 43                            141
  T4                                  9                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED    50  13  11   3
  DEL PEAK  1(1P36.11) WILD-TYPE 174  29  64   5
D34V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           50                            174
  N1                           13                             29
  N2                           11                             64
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    39   3
  DEL PEAK  1(1P36.11) WILD-TYPE 146   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     39    3
  DEL PEAK  1(1P36.11) WILD-TYPE  146    7
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           39                            146
  1                            3                              7
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    21  64
  DEL PEAK  1(1P36.11) WILD-TYPE  80 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     21   64
  DEL PEAK  1(1P36.11) WILD-TYPE   80  224
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           21                             80
  MALE                             64                            224
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       5                         7    71
  DEL PEAK  1(1P36.11) WILD-TYPE    37                        14   240
D34V11, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               71
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3  75
  DEL PEAK  1(1P36.11) WILD-TYPE   6 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3   75
  DEL PEAK  1(1P36.11) WILD-TYPE    6  277
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            277
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  2(1Q32.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1Q32.1) MUTATED    44  27
  DEL PEAK  2(1Q32.1) WILD-TYPE 186 126
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           312 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           27                           126 
$`DEL PEAK  2(1Q32.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
       22.29        16.77        15.12        32.84        14.89         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A2HX 
       12.82         9.96         0.43         4.90        16.31         1.81 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 
       87.32         2.20         7.82        17.72        50.27        48.00 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A85H 
       15.68        30.67        12.03         0.49         2.24        12.95 
TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TE 
       23.41        19.79        18.08         6.28        13.35        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31        31.07        15.95        20.12        17.62        64.44 
TCGA-GC-A3RC TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
       15.91        20.05         5.62        21.34        19.82         8.48 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V 
        8.58        22.72         3.45        11.80        15.58        13.48 
TCGA-S5-A6DX TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HF 
        1.84        17.62        76.01         4.54         6.58        97.12 
TCGA-XF-A8HH TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMX 
        1.87         2.10        10.82       110.60        71.57         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R3 
       44.32        61.45        18.81        11.97        13.64        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-AA5H 
       30.28        74.56        52.73        82.49        19.17 

$`DEL PEAK  2(1Q32.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       20.48         4.67        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E 
       12.92         7.20         5.46         5.19         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62        15.62        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        7.79       123.85        13.58         8.22        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        76.60        67.36        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        43.50        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        24.30        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       20.91         3.62        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       19.33         5.36         5.69         8.25        27.45        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        2.70         7.10        62.86        18.81         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         3.06         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        35.24        33.01         7.23        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       19.46        21.40         2.24        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
       11.31        11.31         7.63        27.09         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI 
       32.98         7.00        14.27        19.10        20.28        10.59 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.35        19.07         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22        25.02        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.38        15.32        21.07        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        31.56        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       67.79        65.75         3.58       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       17.82         1.64        45.04        97.45       125.49        15.35 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        56.48        30.94        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       21.11        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.60        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15         5.52        10.13 

  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                       110.60                        166.03 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                        15.91                         15.60 
[1] "0.4 - 110.6 (15.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1"  
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q32.1) MUTATED         0       28        17       25
  DEL PEAK  2(1Q32.1) WILD-TYPE       4       96       110      104
D35V3, multiclass
           clus
vv          DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           28                            96
  STAGE III                          17                           110
  STAGE IV                           25                           104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  2(1Q32.1) MUTATED         21  31   9
  DEL PEAK  2(1Q32.1) WILD-TYPE      100 153  44
D35V4, multiclass
          clus
vv         DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  T0+T1+T2                          21                           100
  T3                                31                           153
  T4                                 9                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  2(1Q32.1) MUTATED    31   5  19   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 193  37  56   6
D35V5, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  N0                          31                           193
  N1                           5                            37
  N2                          19                            56
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    29   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 156   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     29    2
  DEL PEAK  2(1Q32.1) WILD-TYPE  156    8
   clus
vv  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  0                          29                           156
  1                           2                             8
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    14  57
  DEL PEAK  2(1Q32.1) WILD-TYPE  87 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     14   57
  DEL PEAK  2(1Q32.1) WILD-TYPE   87  231
        clus
vv       DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          14                            87
  MALE                            57                           231
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q32.1) MUTATED       6                         2    60
  DEL PEAK  2(1Q32.1) WILD-TYPE    36                        19   251
D35V11, multiclass
                           clus
vv                          DEL PEAK  2(1Q32.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              60
                           clus
vv                          DEL PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                36
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED     3  65
  DEL PEAK  2(1Q32.1) WILD-TYPE   6 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED      3   65
  DEL PEAK  2(1Q32.1) WILD-TYPE    6  287
                        clus
vv                       DEL PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    73  51
  DEL PEAK  3(2Q22.1) WILD-TYPE 157 102
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          124                           259 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           51                           102 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7S 
       22.29        91.63       103.50         8.35        16.27        34.98 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V 
       15.12        47.80         7.33        17.88        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-C4-A0F6 
        8.35        17.16         4.67        12.82         8.98        23.01 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 
       12.62        12.10        12.92         5.46         5.19        21.86 
TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV 
       18.41         1.81        10.59         2.20        50.27         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U 
       17.98        64.18        67.36        30.67        15.02        10.49 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97P 
       10.62        38.83        17.39         0.92        13.68        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR 
        8.09         8.94        27.98        24.30        19.79        26.73 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF 
        5.36        27.45        18.08         2.70        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.06         4.31        17.23         6.48        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RD 
       26.93        17.62        66.02         6.94        15.81        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        0.49         8.94         2.10        20.98         2.20        11.31 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       27.09         4.73        10.65        14.27        21.34        19.82 
TCGA-GV-A3QK TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ 
       27.35         8.22         3.45         9.14         1.74         1.81 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78N 
       11.80        15.58        13.48         3.75        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH 
       76.01        65.75        17.82         6.58        15.35         1.87 
TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG 
       12.76        26.27        66.64        13.74        10.82       110.60 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
        2.96         6.77        61.45        75.39         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       13.64        18.64        21.11        24.13        28.41        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X 
       52.60        47.84        20.22        34.06         8.61        63.02 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       57.90        19.40         8.52        19.17 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       11.97       105.70        44.94        16.83        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       10.22        33.83        40.08         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        13.15        19.04        32.84        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK 
        5.06        14.96         8.25        16.18        20.48         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.56        28.70        24.26        28.41         1.94         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.00        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       13.08         4.90         7.20        16.31         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.14        17.62        15.62         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82         8.22        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       140.81        48.00        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        38.24        13.58       166.03        12.36 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC 
        8.65         7.53        13.64        43.50        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.22        14.07        12.95        15.32        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SL 
       33.04         4.01        12.62        22.52        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       17.98        29.16         5.52        25.74        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       53.88        11.01        19.33         5.69         8.25        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25        15.95        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
       20.12        64.44        19.46        21.40         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        17.75        24.92        13.91         7.73         3.12 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        7.36        10.92        11.31         7.63        20.05         5.62 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       32.98         7.00        19.10        20.28         8.48        10.59 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        3.06         9.01        25.02        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
        9.07        11.70        15.42         6.38        15.32        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       17.62        37.05        67.79         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       29.56         4.54         1.64        45.04        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       97.12        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       66.41        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        16.27         2.10        92.98        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ 
        7.63        71.57        91.73         8.32        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       56.48        30.94        86.30        27.06        18.81         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.84         9.63         7.36        30.28        27.19        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4T 
       74.56        13.41         3.48        82.49         2.89        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       59.38        60.16        38.73        35.41        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       110.60                        166.03 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        15.07                         16.14 
[1] "0.5 - 110.6 (15.1)" "0.1 - 166.0 (16.1)"
[1] "hr=" "1.1"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         1       39        43       43
  DEL PEAK  3(2Q22.1) WILD-TYPE       3       85        84       86
D36V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             1                             3
  STAGE II                           39                            85
  STAGE III                          43                            84
  STAGE IV                           43                            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED         35  63  16
  DEL PEAK  3(2Q22.1) WILD-TYPE       86 121  37
D36V4, multiclass
          clus
vv         DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1+T2                          35                            86
  T3                                63                           121
  T4                                16                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  3(2Q22.1) MUTATED    65  12  28   3
  DEL PEAK  3(2Q22.1) WILD-TYPE 159  30  47   5
D36V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                          65                           159
  N1                          12                            30
  N2                          28                            47
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    61   5
  DEL PEAK  3(2Q22.1) WILD-TYPE 124   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     61    5
  DEL PEAK  3(2Q22.1) WILD-TYPE  124    5
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          61                           124
  1                           5                             5
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    38  88
  DEL PEAK  3(2Q22.1) WILD-TYPE  63 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     38   88
  DEL PEAK  3(2Q22.1) WILD-TYPE   63  200
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          38                            63
  MALE                            88                           200
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED      11                         7   101
  DEL PEAK  3(2Q22.1) WILD-TYPE    31                        14   210
D36V11, multiclass
                           clus
vv                          DEL PEAK  3(2Q22.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             101
                           clus
vv                          DEL PEAK  3(2Q22.1) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     4 114
  DEL PEAK  3(2Q22.1) WILD-TYPE   5 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      4  114
  DEL PEAK  3(2Q22.1) WILD-TYPE    5  238
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           238
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  4(2Q34) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2Q34) MUTATED    97  62
  DEL PEAK  4(2Q34) WILD-TYPE 133  91
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        159                         224 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                         62                          91 
$`DEL PEAK  4(2Q34) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       17.16        34.98         0.62        15.12        10.22        47.80 
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
        2.66        19.04        32.84        14.89         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS 
       17.16         4.67        28.70        24.26         8.98         0.43 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       12.62        12.10        11.87        12.92         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.31         2.14       130.88         1.81        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
        2.20        13.58         7.82        50.27        21.30         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        64.18        41.56        67.36        41.06        30.67 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.02        10.49        12.03        10.62        15.35        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97P 
        0.49        17.39         0.92         1.22        13.68        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN 
        8.09        16.77         8.94        22.52        24.30        29.16 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.79        26.73         5.36         8.25        27.45        18.08 
TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        2.70        12.69        12.36         2.27         3.06         4.31 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3VY 
       17.23         6.48        61.94        15.95        26.93        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       66.02        64.44        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO 
       24.92         0.49         2.10        10.92         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       14.27        21.34         8.48        10.59        27.35        19.07 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       22.72        38.60         8.22        25.02         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO 
        9.14        27.68         9.07         1.74         1.81        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       15.32        15.58        13.48        16.67         3.75        17.62 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        86.83        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SJ TCGA-XF-A9SV 
        4.54         1.64        15.35         1.87         3.22        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T8 
       11.90        23.64        21.04        26.27         2.24        13.74 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 
       10.82       110.60         2.96        44.32        61.45        18.81 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       11.97        18.64        21.11        24.13        28.41        74.56 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4V 
        3.48        52.73        52.60        47.84        34.06        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA5H 
       63.02        57.90        19.17 

$`DEL PEAK  4(2Q34) WILD-TYPE`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      103.50        44.94        16.83        16.77        27.62        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       41.75        51.16        66.54        33.83        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         9.96        17.56        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM 
       12.26        13.12        12.00        11.34        11.34        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        4.90         7.20         1.84        13.58        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
       15.62       123.85        87.32         8.22        17.72        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-A6B2 
       20.81        10.55       140.81        48.00        76.60        15.68 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       38.24        13.58       166.03        12.36         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       13.64        43.50        43.59        38.83         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B6 
       14.33        14.07        12.95        15.32        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        27.98        60.66        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        18.81         6.15         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO 
        7.13        10.65         8.94         3.25        30.61        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       33.01         7.23        20.12         6.94        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        2.24        15.91         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20         7.36        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX 
       27.09        20.05         5.62        32.98         7.00        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
       19.82        20.28         8.58         1.51        19.40         3.06 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT 
        9.01         2.76        11.70        15.42         6.38        21.07 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       12.23        14.24         1.84        12.43        31.56        37.05 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HC 
       76.01        67.79         3.58       112.83        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49        97.12        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       79.66        66.41        28.24        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        92.98        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         8.32         6.77        98.99        56.48        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66        13.64         7.36        30.28        27.19        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       13.41        82.49        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                       0.43                        0.10 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                     130.88                      166.03 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                     15.350                      16.025 
[1] "0.4 - 130.9 (15.3)" "0.1 - 166.0 (16.0)"
[1] "hr=" "1.1"
D37V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q34) MUTATED         1       50        49       59
  DEL PEAK  4(2Q34) WILD-TYPE       3       74        78       70
D37V3, multiclass
           clus
vv          DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  STAGE I                           1                           3
  STAGE II                         50                          74
  STAGE III                        49                          78
  STAGE IV                         59                          70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2  T3  T4
  DEL PEAK  4(2Q34) MUTATED         45  81  20
  DEL PEAK  4(2Q34) WILD-TYPE       76 103  33
D37V4, multiclass
          clus
vv         DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  T0+T1+T2                        45                          76
  T3                              81                         103
  T4                              20                          33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  4(2Q34) MUTATED    86  14  42   3
  DEL PEAK  4(2Q34) WILD-TYPE 138  28  33   5
D37V5, multiclass
    clus
vv   DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  N0                        86                         138
  N1                        14                          28
  N2                        42                          33
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED    74   4
  DEL PEAK  4(2Q34) WILD-TYPE 111   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED     74    4
  DEL PEAK  4(2Q34) WILD-TYPE  111    6
   clus
vv  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  0                        74                         111
  1                         4                           6
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED    37 124
  DEL PEAK  4(2Q34) WILD-TYPE  64 164
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED     37  124
  DEL PEAK  4(2Q34) WILD-TYPE   64  164
        clus
vv       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  FEMALE                        37                          64
  MALE                         124                         164
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q34) MUTATED      13                         9   134
  DEL PEAK  4(2Q34) WILD-TYPE    29                        12   177
D37V11, multiclass
                           clus
vv                          DEL PEAK  4(2Q34) MUTATED
  ASIAN                                            13
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                           134
                           clus
vv                          DEL PEAK  4(2Q34) WILD-TYPE
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED     5 144
  DEL PEAK  4(2Q34) WILD-TYPE   4 208
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED      5  144
  DEL PEAK  4(2Q34) WILD-TYPE    4  208
                        clus
vv                       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  HISPANIC OR LATINO                             5                           4
  NOT HISPANIC OR LATINO                       144                         208
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.1) MUTATED   119  76
  DEL PEAK  5(2Q37.1) WILD-TYPE 111  77
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          195                           188 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           76                            77 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       17.16        34.98         0.62        15.12        10.22        47.80 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T 
       40.08         2.66        19.04        32.84        19.50        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.35         8.25        17.16         4.67        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X 
       28.70        24.26         8.98         0.46         0.43        12.62 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.10        11.34        11.87        12.92         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19        16.31         1.84         2.14       130.88       112.44 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62         1.81        10.59         2.20        13.58         7.82 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30        23.21         9.67        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        67.36        41.06        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 
      166.03        10.49         7.53        13.64        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        38.83        24.66         0.49        17.39         0.56 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
        0.92         1.22        13.68        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
        8.94        22.52        24.30        29.16        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        3.62        26.73         5.36         8.25        27.45        18.08 
TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        2.70         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        4.31        17.23         6.48        61.94        15.95        26.93 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
       17.62        66.02        64.44        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OP 
       15.91        14.07        17.75        24.92         0.49         2.10 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
       10.92         7.63         4.73        10.65        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        22.72        38.60         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
        3.45        21.24         9.14        27.68         9.07         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        15.42        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       16.67         1.84         3.75        31.56        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH 
        4.54         1.64        45.04         6.58        15.35         1.87 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
        3.22        12.76        11.90        23.64        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
        2.24        13.74        10.82       110.60         2.96         8.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       30.94        61.45        18.81        11.97        13.64        18.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.11        24.13        28.41        74.56         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       52.60        47.84        20.22        34.06         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA5H 
       63.02        57.90        19.17 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      103.50        44.94        16.83        16.77        27.62        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM 
       41.75        51.16        66.54        33.83         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
       12.39         6.58        13.15        12.16        17.88         5.06 
TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F 
       14.96        16.18        20.48        12.82         9.96        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FM 
       12.10        12.26        13.12        12.00        11.34        13.08 
TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        4.90        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.70        16.14        17.62         7.79       123.85        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
        8.22        17.72        20.81        10.55       140.81        48.00 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA74 
       76.60        15.68        13.58        12.36         8.65        43.50 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       43.59         0.10         2.24        16.70         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       13.97        12.99        14.33        14.07        12.95        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       32.02        33.04         4.01        12.62        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N 
       23.41        17.98         5.52        25.74        46.78        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       62.86        18.81         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
       10.65         8.94         3.25        30.61        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A6I1 
        7.23        20.12         6.94        21.40         2.24         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ 
       11.31        11.31        27.09        20.05         5.62         7.00 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A4AB 
       19.82         8.58         1.51        19.40         3.06         2.76 
TCGA-K4-A5RI TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-SY-A9G0 
       11.70         6.38        21.07        12.23        14.24        12.43 
TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HD TCGA-XF-A8HE 
       37.05        67.79         3.58       112.83        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       97.12        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90        16.27        66.64         2.10        92.98 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX 
       11.31        54.90         7.63        71.57        91.73         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        56.48        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R4 
        3.88        18.84         9.63         0.66         7.36        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4T 
       27.19        21.86        13.41        82.49         2.89        19.69 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       15.420                        16.225 
[1] "0.4 - 166.0 (15.4)" "0.1 - 140.8 (16.2)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED         2       62        58       72
  DEL PEAK  5(2Q37.1) WILD-TYPE       2       62        69       57
D38V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           62                            62
  STAGE III                          58                            69
  STAGE IV                           72                            57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  5(2Q37.1) MUTATED         60 93 29
  DEL PEAK  5(2Q37.1) WILD-TYPE       61 91 24
D38V4, multiclass
          clus
vv         DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T0+T1+T2                          60                            61
  T3                                93                            91
  T4                                29                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  5(2Q37.1) MUTATED   106  19  50   3
  DEL PEAK  5(2Q37.1) WILD-TYPE 118  23  25   5
D38V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                         106                           118
  N1                          19                            23
  N2                          50                            25
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.1) MUTATED   95  4
  DEL PEAK  5(2Q37.1) WILD-TYPE 90  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     95    4
  DEL PEAK  5(2Q37.1) WILD-TYPE   90    6
   clus
vv  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  0                          95                            90
  1                           4                             6
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    43 155
  DEL PEAK  5(2Q37.1) WILD-TYPE  58 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     43  155
  DEL PEAK  5(2Q37.1) WILD-TYPE   58  133
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          43                            58
  MALE                           155                           133
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED      18                         9   161
  DEL PEAK  5(2Q37.1) WILD-TYPE    24                        12   150
D38V11, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             161
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     7 177
  DEL PEAK  5(2Q37.1) WILD-TYPE   2 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      7  177
  DEL PEAK  5(2Q37.1) WILD-TYPE    2  175
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         177
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           175
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    63  47
  DEL PEAK  6(3P14.2) WILD-TYPE 167 106
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          110                           273 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           47                           106 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 
       22.29       103.50         8.35        16.77        27.62        51.16 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42C 
       14.89         5.06         8.35         8.25        17.56        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR 
       24.26         8.98         1.94         0.43        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
        5.46        16.31        66.41        16.70         7.79         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6B5 TCGA-DK-AA6L 
       17.72        50.27        10.55        48.00        41.06        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A7DV 
       13.58         8.65        10.62        43.59        17.39         1.22 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       12.95         8.09        16.77        33.04        22.52        24.30 
TCGA-FD-A3SN TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       29.16        22.98        15.58         5.36         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF 
       58.92         6.28         2.27         3.06        10.65        61.94 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       30.61        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A6C6 
       19.46         2.24         4.50        17.75        24.92         2.20 
TCGA-GU-A42Q TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-H4-A2HQ 
       11.31         4.73         7.00        21.34        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI 
       38.60         9.01        25.02        21.24         9.14        11.70 
TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P 
       15.42        12.23        16.67        31.56        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A8HI 
       65.75         3.58       112.83        29.56        97.45        17.88 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMQ 
       26.27        66.64         2.10        13.74       110.60        71.57 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R9 TCGA-ZF-A9RD 
        2.96         8.32        86.30        13.64        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA53 
        3.48        52.73        52.60        34.06        60.16        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        19.17 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        91.63       105.70        16.27        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 
       17.16        34.98        49.12         0.62        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41        23.01         0.46         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO 
       12.10        11.34        11.34        11.87        13.08         4.90 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.19         1.84        13.58        21.86         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        8.22        21.30        23.21         9.67        20.81       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       30.67        15.02       166.03        12.36        10.49         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        12.03        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 
       14.07        15.32        14.37        32.02         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       12.62        27.98        60.66        23.41        17.98         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        19.79        12.85        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        5.69        18.08         2.70         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81         6.15        12.69        12.36         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3C TCGA-G2-AA3D 
        6.48        15.95        26.93        35.24         6.94        64.44 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       21.40        15.81        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
       13.91         7.73         2.10         3.12        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       10.92        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        19.07         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
        3.06         8.22         3.45         2.76        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        13.48        14.24         1.84         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PD 
       17.62        37.05        22.68        86.83        35.24        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF 
        4.54         1.64        45.04         6.58       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       15.35         1.87        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24        16.27        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        91.73         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       74.56        82.49        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        8.61        59.38        63.02        38.73        35.41        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15         5.52        10.13 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       112.83                        166.03 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                        17.59                         15.12 
[1] "0.4 - 112.8 (17.6)" "0.1 - 166.0 (15.1)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P14.2) MUTATED         0       31        38       39
  DEL PEAK  6(3P14.2) WILD-TYPE       4       93        89       90
D39V3, multiclass
           clus
vv          DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           31                            93
  STAGE III                          38                            89
  STAGE IV                           39                            90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  6(3P14.2) MUTATED         31  58  13
  DEL PEAK  6(3P14.2) WILD-TYPE       90 126  40
D39V4, multiclass
          clus
vv         DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T0+T1+T2                          31                            90
  T3                                58                           126
  T4                                13                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(3P14.2) MUTATED    62  18  16   5
  DEL PEAK  6(3P14.2) WILD-TYPE 162  24  59   3
D39V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  N0                          62                           162
  N1                          18                            24
  N2                          16                            59
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    43   4
  DEL PEAK  6(3P14.2) WILD-TYPE 142   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     43    4
  DEL PEAK  6(3P14.2) WILD-TYPE  142    6
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          43                           142
  1                           4                             6
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    39  72
  DEL PEAK  6(3P14.2) WILD-TYPE  62 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     39   72
  DEL PEAK  6(3P14.2) WILD-TYPE   62  216
        clus
vv       DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  FEMALE                          39                            62
  MALE                            72                           216
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P14.2) MUTATED       3                         7    95
  DEL PEAK  6(3P14.2) WILD-TYPE    39                        14   216
D39V11, multiclass
                           clus
vv                          DEL PEAK  6(3P14.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              95
                           clus
vv                          DEL PEAK  6(3P14.2) WILD-TYPE
  ASIAN                                                39
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               216
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED     5  97
  DEL PEAK  6(3P14.2) WILD-TYPE   4 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      5   97
  DEL PEAK  6(3P14.2) WILD-TYPE    4  255
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           255
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    82  70
  DEL PEAK  7(4Q22.1) WILD-TYPE 148  83
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          152                           231 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           70                            83 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 
      105.70         8.35        16.77        17.16         0.62        51.16 
TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB 
       10.22         7.33         5.06        14.96         5.06        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
       20.48         4.67        12.82        17.56        28.70        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47V TCGA-CU-A0YN 
        1.94        23.01         0.46         0.43        12.46        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX 
        4.90         7.20        21.86        18.41       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59         7.79        87.32         2.20         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.72        21.30        17.98        64.18        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E5-A4TZ 
       30.67        38.24        13.58         8.65        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B3 TCGA-FD-A3B6 
       38.83        24.66        17.39         0.92        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BR 
        4.01        24.30        23.41         5.52        15.58        26.73 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15         3.06         4.31        10.85        31.07        17.23 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3D 
       61.94        26.93        35.24        33.01         7.23        64.44 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       21.40        15.81         4.50         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP 
        7.73         2.20        11.31         7.63        20.05        32.98 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS 
       14.27         8.48        22.72        19.40         3.06        25.02 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 
        1.81        15.42        12.23        16.67        14.24        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       31.56        17.62        22.68        86.83        76.01        65.75 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
      112.83        35.24        29.56         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T5 
       97.12        15.35        48.62        23.64        26.27        66.64 
TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
       13.74       110.60        54.90         2.96         8.32        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
       44.32        56.48        61.45        86.30        18.81        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       18.64        30.28        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       52.73        52.60        82.49        20.22         2.89         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA54 
       63.02        19.40 

$`DEL PEAK  7(4Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.83        34.98        27.62        49.12        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        47.80        33.83        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89         8.35         8.25        17.16 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        9.96        24.26         8.98         0.69        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.34        11.87        13.08         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         1.84        13.58         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
       16.70       130.88        16.14        17.62        15.62       123.85 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       13.58        50.27        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6P 
      140.81        48.00        41.56        76.60        67.36        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        12.36        10.49         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        10.62         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       60.66        17.98        29.16        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       18.08        62.86        18.81        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        9.67         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       30.61        15.95        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46         2.24        15.91        14.07        17.75        24.92 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         7.36        10.92        11.31 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.07         1.51        38.60         9.01         8.22         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        2.76         6.38        11.80        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC 
       13.48         1.84         3.75        37.05        67.79         3.58 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82        45.04        97.45       125.49         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       21.04        28.24        18.90         2.24        16.27         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       92.98        10.82        11.31         7.63        71.57        91.73 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        30.94        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        9.63         0.66        11.97         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       27.19        28.41        47.84        34.06        19.69        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        38.73        35.41        57.90         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       112.83                        166.03 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       16.965                        15.120 
[1] "0.4 - 112.8 (17.0)" "0.1 - 166.0 (15.1)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q22.1) MUTATED         0       44        51       56
  DEL PEAK  7(4Q22.1) WILD-TYPE       4       80        76       73
D40V3, multiclass
           clus
vv          DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           44                            80
  STAGE III                          51                            76
  STAGE IV                           56                            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  7(4Q22.1) MUTATED         43  82  16
  DEL PEAK  7(4Q22.1) WILD-TYPE       78 102  37
D40V4, multiclass
          clus
vv         DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T0+T1+T2                          43                            78
  T3                                82                           102
  T4                                16                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  7(4Q22.1) MUTATED    81  20  33   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 143  22  42   6
D40V5, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  N0                          81                           143
  N1                          20                            22
  N2                          33                            42
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    68   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 117   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     68    2
  DEL PEAK  7(4Q22.1) WILD-TYPE  117    8
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          68                           117
  1                           2                             8
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    43 111
  DEL PEAK  7(4Q22.1) WILD-TYPE  58 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     43  111
  DEL PEAK  7(4Q22.1) WILD-TYPE   58  177
        clus
vv       DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  FEMALE                          43                            58
  MALE                           111                           177
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q22.1) MUTATED      10                        10   128
  DEL PEAK  7(4Q22.1) WILD-TYPE    32                        11   183
D40V11, multiclass
                           clus
vv                          DEL PEAK  7(4Q22.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             128
                           clus
vv                          DEL PEAK  7(4Q22.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED     5 140
  DEL PEAK  7(4Q22.1) WILD-TYPE   4 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      5  140
  DEL PEAK  7(4Q22.1) WILD-TYPE    4  212
                        clus
vv                       DEL PEAK  7(4Q22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         140
                        clus
vv                       DEL PEAK  7(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           212
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  8(4Q34.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q34.2) MUTATED    96  71
  DEL PEAK  8(4Q34.2) WILD-TYPE 134  82
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          167                           216 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                           71                            82 
$`DEL PEAK  8(4Q34.2) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 
      105.70         8.35        16.77        17.16         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       15.12        10.22         2.66        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.35        16.18        20.48         4.67        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70        24.26        28.41         1.94         0.46         0.43 
TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 
       10.95        12.92         4.90         7.20        21.86        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
      112.44        16.14         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 
        2.20         7.82         8.22        21.30        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6W 
       41.06        30.67        38.24        13.58       166.03         8.65 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A85H 
       10.62        43.59        15.35        17.39         0.92        12.95 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO 
       32.02        33.04         4.01        23.41        29.16         5.52 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       22.98        15.58        26.73         8.25        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31        10.85        31.07 
TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       17.23        61.94        26.93         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02        64.44        19.46        21.40        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.91        17.75        13.91         7.73         2.20        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
        7.63        20.05        32.98        14.27        21.34         8.48 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.07        22.72        19.40        38.60         3.06        25.02 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
        1.81        15.42        15.58        13.48        16.67        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        31.56        17.62        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       67.79        65.75       112.83        35.24        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
        1.64        45.04         6.58        97.12        15.35         3.22 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMG 
       23.64        21.04        26.27        66.64        10.82       110.60 
TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       54.90         2.96         8.32         6.77        98.99        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 
       61.45        86.30        18.81        13.64        18.64        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4N 
       21.86        74.56        13.41         3.48        52.60         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA5H 
       19.69         8.61        63.02        19.40        19.17 

$`DEL PEAK  8(4Q34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.83        34.98        27.62        49.12        41.75        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        33.83        40.08         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       14.96         8.25        17.16        12.82         9.96         8.98 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       23.01         0.69        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.87        13.08         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       17.62        15.62       123.85        13.58        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6P TCGA-DK-AA6T 
       17.98        41.56        76.60        67.36        15.02        12.36 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4U1 
       10.49         7.53        13.64        43.50        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       24.66         0.10         0.49         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66        14.56        13.97        12.99        14.33         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        25.74        46.78        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        20.91         3.62        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-FD-A6TI 
        5.36         5.69        27.45        18.08        18.81         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
        7.13        10.65         8.94         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RD 
       15.95        35.24        33.01         6.94         2.24        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         0.49         8.94         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.36        10.92        11.31        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       10.65         7.00        19.10        19.82        20.28        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       27.35         8.58         1.51         9.01         8.22         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
        2.76         6.38        11.80        15.32        21.07        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HD 
        1.84         3.75        37.05         3.58        17.82        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       66.41        12.76        11.90        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAML 
       16.27         2.10        13.74        92.98        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       71.57        91.73        44.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        11.97         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RL 
       21.11        24.13        27.19        28.41        52.73        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       47.84        20.22        34.06        59.38        60.16        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        57.90         8.52        47.15         5.52        10.13 

  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                        16.67                         14.96 
[1] "0.4 - 166.0 (16.7)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(4Q34.2) MUTATED         0       47        53       65
  DEL PEAK  8(4Q34.2) WILD-TYPE       4       77        74       64
D41V3, multiclass
           clus
vv          DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           47                            77
  STAGE III                          53                            74
  STAGE IV                           65                            64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  8(4Q34.2) MUTATED         45 90 19
  DEL PEAK  8(4Q34.2) WILD-TYPE       76 94 34
D41V4, multiclass
          clus
vv         DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  T0+T1+T2                          45                            76
  T3                                90                            94
  T4                                19                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(4Q34.2) MUTATED    87  22  41   1
  DEL PEAK  8(4Q34.2) WILD-TYPE 137  20  34   7
D41V5, multiclass
    clus
vv   DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  N0                          87                           137
  N1                          22                            20
  N2                          41                            34
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED    68   4
  DEL PEAK  8(4Q34.2) WILD-TYPE 117   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED     68    4
  DEL PEAK  8(4Q34.2) WILD-TYPE  117    6
   clus
vv  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  0                          68                           117
  1                           4                             6
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED    45 124
  DEL PEAK  8(4Q34.2) WILD-TYPE  56 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED     45  124
  DEL PEAK  8(4Q34.2) WILD-TYPE   56  164
        clus
vv       DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  FEMALE                          45                            56
  MALE                           124                           164
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.2) MUTATED      12                        11   140
  DEL PEAK  8(4Q34.2) WILD-TYPE    30                        10   171
D41V11, multiclass
                           clus
vv                          DEL PEAK  8(4Q34.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             140
                           clus
vv                          DEL PEAK  8(4Q34.2) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED     6 152
  DEL PEAK  8(4Q34.2) WILD-TYPE   3 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED      6  152
  DEL PEAK  8(4Q34.2) WILD-TYPE    3  200
                        clus
vv                       DEL PEAK  8(4Q34.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         152
                        clus
vv                       DEL PEAK  8(4Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED   104  83
  DEL PEAK  9(5Q12.1) WILD-TYPE 126  70
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          187                           196 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           83                            70 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       22.29        11.97       105.70         8.35        16.83        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I 
       17.16        27.62        15.12        10.22        40.08         7.33 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        6.58        19.04        32.84         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A8HY 
       17.56        24.26        23.01         0.46         0.43        11.34 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 
        5.19         2.14        18.41       112.44        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 
       50.27        21.30        23.21         9.67        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       17.98        64.18        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-E5-A2PC 
       13.58       166.03        10.49         8.65         7.53        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME 
       15.35        38.83        24.66         0.49        17.39        12.99 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.92         1.22        13.68         8.09         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR 
       22.52        24.30        23.41        17.98        25.74        19.79 
TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.85        20.91        26.73         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08         2.70         7.10        13.35        18.81         6.15 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.27         3.06        10.85        31.07        10.65        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B 
        6.48        61.94        26.93         7.23        17.62        66.02 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       19.46        15.81        24.92         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        7.73         2.10         2.20         7.36        10.92         7.63 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98         7.00        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        10.59         8.58        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.40        38.60         3.06         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ 
       21.24         2.76         9.14        27.68        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 
       15.42        11.80        13.48        16.67        14.24        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       17.62        37.05        22.68        65.75       112.83        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       17.82         4.54         1.64         6.58        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMJ 
        3.22        12.76        23.64        28.24         2.24        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-YF-AA3L 
        7.63         2.96         6.77        44.32        56.48        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       13.64        18.64         7.36        24.13        21.86        28.41 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 
       59.38        63.02        38.73        35.41        57.90         8.52 
TCGA-ZF-AA5H 
       19.17 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       91.63       103.50        16.27        44.94        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 
        0.62        41.75        51.16        66.54        47.80        33.83 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        12.39        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
       19.50        14.96         8.25         9.96        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98         1.94         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.46        16.31         1.84        13.58        21.86        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        1.81         7.79        20.81       140.81        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       67.36        30.67        12.36        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       10.62         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.56        13.97        14.33        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.37        32.02        16.77         4.01        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P 
       60.66        29.16         5.52        46.78        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        15.58        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69        58.92         6.28        62.86        12.69        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ 
        4.31         9.67         7.13         8.94         3.25        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D 
       15.95        35.24        33.01        20.12         6.94        64.44 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40         2.24         4.50        15.91        14.07        17.75 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        3.12        20.98        11.31        11.31        27.09        20.05 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS 
        5.62        14.27        19.82        27.35         1.51        25.02 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        9.07         1.74         6.38        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A78O 
       12.23         1.84         3.75        12.43        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       67.79         3.58        35.24        45.04        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73         8.32        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC 
        9.63         0.66        21.11        30.28        27.19        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA4W 
       13.41         3.48        52.73        52.60         8.61        60.16 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40        47.15         5.52        10.13 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        15.81                         15.60 
[1] "0.4 - 166.0 (15.8)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.4"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(5Q12.1) MUTATED         2       53        56       75
  DEL PEAK  9(5Q12.1) WILD-TYPE       2       71        71       54
D42V3, multiclass
           clus
vv          DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           53                            71
  STAGE III                          56                            71
  STAGE IV                           75                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  9(5Q12.1) MUTATED         51 97 24
  DEL PEAK  9(5Q12.1) WILD-TYPE       70 87 29
D42V4, multiclass
          clus
vv         DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T0+T1+T2                          51                            70
  T3                                97                            87
  T4                                24                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  9(5Q12.1) MUTATED    90  24  46   6
  DEL PEAK  9(5Q12.1) WILD-TYPE 134  18  29   2
D42V5, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          90                           134
  N1                          24                            18
  N2                          46                            29
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    85   7
  DEL PEAK  9(5Q12.1) WILD-TYPE 100   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     85    7
  DEL PEAK  9(5Q12.1) WILD-TYPE  100    3
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          85                           100
  1                           7                             3
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    50 140
  DEL PEAK  9(5Q12.1) WILD-TYPE  51 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     50  140
  DEL PEAK  9(5Q12.1) WILD-TYPE   51  148
        clus
vv       DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  FEMALE                          50                            51
  MALE                           140                           148
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED      14                        12   155
  DEL PEAK  9(5Q12.1) WILD-TYPE    28                         9   156
D42V11, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             155
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     4 173
  DEL PEAK  9(5Q12.1) WILD-TYPE   5 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      4  173
  DEL PEAK  9(5Q12.1) WILD-TYPE    5  179
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         173
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           179
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 10(6P25.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P25.3) MUTATED    54  42
  DEL PEAK 10(6P25.3) WILD-TYPE 176 111
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           96                           287 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           42                           111 
$`DEL PEAK 10(6P25.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BT-A20V TCGA-BT-A20X 
        8.35        16.77        17.16        51.16         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-CU-A0YR TCGA-CU-A5W6 
       17.16        16.18        20.48         4.67         7.20         1.84 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 
       13.58        66.41        16.70       130.88         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 
        7.79       123.85        13.58        21.30        48.00        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 
       67.36        30.67        15.02        10.49        13.64        12.03 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q 
       15.35        38.83         0.49        13.68        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN 
       16.77        33.04         4.01        60.66        23.41        29.16 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62P TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       20.91         5.36         7.10         6.28        31.07        17.23 
TCGA-G2-A2EO TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3JZ 
       35.24        13.91         2.10        20.98        20.05        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HQ 
       20.28         8.48        10.59        27.35         8.58        19.40 
TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        3.06         2.76        11.70         1.81        15.58        13.48 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78N TCGA-UY-A8OD TCGA-XF-A8HG 
       12.23        14.24        17.62        86.83       112.83        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMG 
        1.87        48.62        28.24        26.27        10.82       110.60 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       56.48        86.30        75.39        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 
       21.11        74.56         2.89        59.38        38.73        57.90 

$`DEL PEAK 10(6P25.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        34.98        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06        14.89        14.96         8.35        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         5.46         5.19        16.31        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00       112.44        16.14        17.62        15.62 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         7.82         8.22        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV 
       23.21         9.67        20.81        10.55       140.81        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       41.56        76.60        15.68        41.06        38.24        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 
      166.03        12.36         8.65         7.53        43.50        10.62 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       43.59        24.66         0.10         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 
        0.92         1.22        14.07        12.95        15.32        32.02 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SM 
        8.94        12.62        22.52        27.98        24.30        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       58.92         2.70        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       10.85         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75        24.92         0.49         8.94         7.73         3.12 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       14.27        21.34        19.10        19.07        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14        27.68         9.07         1.74        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        15.32        21.07        16.67         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       12.43        31.56        37.05        22.68        76.01        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       65.75         3.58        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.64        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       17.88        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       11.90        23.64        21.04        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMQ 
       66.64         2.10        13.74        92.98        11.31        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 
       91.73         2.96        30.94        61.45        27.06        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 
        3.88        18.84         9.63         0.66        11.97        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
       19.69         8.61        60.16        63.02        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                       130.88                        166.03 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                       16.735                        15.580 
[1] "0.5 - 130.9 (16.7)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1"  
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6P25.3) MUTATED         1       27        33       36
  DEL PEAK 10(6P25.3) WILD-TYPE       3       97        94       93
D43V3, multiclass
           clus
vv          DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  STAGE I                             1                             3
  STAGE II                           27                            97
  STAGE III                          33                            94
  STAGE IV                           36                            93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 10(6P25.3) MUTATED         24  43  18
  DEL PEAK 10(6P25.3) WILD-TYPE       97 141  35
D43V4, multiclass
          clus
vv         DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  T0+T1+T2                          24                            97
  T3                                43                           141
  T4                                18                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 10(6P25.3) MUTATED    49   6  24   3
  DEL PEAK 10(6P25.3) WILD-TYPE 175  36  51   5
D43V5, multiclass
    clus
vv   DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  N0                          49                           175
  N1                           6                            36
  N2                          24                            51
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    47   2
  DEL PEAK 10(6P25.3) WILD-TYPE 138   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     47    2
  DEL PEAK 10(6P25.3) WILD-TYPE  138    8
   clus
vv  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  0                          47                           138
  1                           2                             8
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    30  67
  DEL PEAK 10(6P25.3) WILD-TYPE  71 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     30   67
  DEL PEAK 10(6P25.3) WILD-TYPE   71  221
        clus
vv       DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  FEMALE                          30                            71
  MALE                            67                           221
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.3) MUTATED       5                         9    79
  DEL PEAK 10(6P25.3) WILD-TYPE    37                        12   232
D43V11, multiclass
                           clus
vv                          DEL PEAK 10(6P25.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                              79
                           clus
vv                          DEL PEAK 10(6P25.3) WILD-TYPE
  ASIAN                                                37
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED     4  87
  DEL PEAK 10(6P25.3) WILD-TYPE   5 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED      4   87
  DEL PEAK 10(6P25.3) WILD-TYPE    5  265
                        clus
vv                       DEL PEAK 10(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       DEL PEAK 10(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           265
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 11(6Q21) MUTATION ANALYSIS
D44V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q21) MUTATED   102  78
  DEL PEAK 11(6Q21) WILD-TYPE 128  75
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        180                         203 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                         78                          75 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       16.77        27.62         0.62        41.75        51.16        10.22 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       19.04        32.84        14.89         5.06        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67         9.96        17.56        28.70         1.94         0.46 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
        0.69        12.62         5.19         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41        16.70         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         2.20        13.58        17.72        50.27        21.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       48.00        17.98        64.18        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 
       15.02        13.58       166.03        12.36         8.65        13.64 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       12.03        43.59        15.35        38.83         0.49        17.39 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ 
        0.56        12.99         1.22         8.09         8.94        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY 
       20.91        26.73        11.01        19.33         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08        58.92         7.10         6.28        13.35 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P 
        6.15        12.36         3.06         4.31        31.07         6.48 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       35.24        33.01        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
       19.46         2.24        14.07         0.49         8.94         2.10 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       10.92        11.31         7.63         4.73        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G 
       21.34        19.10        20.28         8.48         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A4AB 
       22.72        19.40        38.60         3.06        21.24         2.76 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       11.70         1.81        15.58        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       65.75       112.83        29.56        17.82         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 
       48.62        79.66         3.22        11.90        28.24        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW 
        2.24         2.10        54.90         7.63        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YF-AA3L 
        6.77        44.32        56.48        86.30        75.39        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       13.64        18.64         7.36        21.11        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X 
       74.56        20.22         2.89        34.06        19.69        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       38.73        35.41        57.90        19.40        47.15        19.17 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KP TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       11.97        44.94        16.83        17.16        34.98        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        15.12        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.66         6.74        12.39         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       17.16        12.82        24.26        28.41         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.43        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       13.08        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       13.58         2.14        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
       17.62        15.62         7.82         8.22        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       20.81        10.55       140.81        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 
       15.68        10.49         7.53        43.50        10.62        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         2.24        16.70         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         0.92        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       22.52        27.98        60.66        17.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX 
       22.98        14.96         3.62        15.58        53.88         5.69 
TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI 
        2.70        62.86        18.81        12.69         2.27         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85         7.13        10.65        17.23         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C 
       61.94        30.61        15.95        26.93         7.23         6.94 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40        15.81         4.50        15.91        17.75        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV 
       11.31        27.09        20.05         5.62        10.65        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.82        10.59        27.35         1.51         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
       25.02         3.45         9.14        27.68         9.07         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
       15.42         6.38        11.80        15.32        21.07        12.23 
TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
        3.75        86.83        76.01        67.79         3.58        35.24 
TCGA-UY-A9PE TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX 
        4.54       125.49        64.80        66.41        12.76        23.64 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       21.04        18.90        16.27        66.64        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMY 
       10.82       110.60        11.31        71.57         2.96        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        61.45        27.06        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RD 
        9.63         0.66        24.13        30.28        27.19        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4U 
        3.48        52.73        52.60        82.49        47.84         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       59.38        60.16         8.52         5.52        10.13 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                       0.46                        0.10 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     166.03                      140.81 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                      17.85                       14.33 
[1] "0.5 - 166.0 (17.9)" "0.1 - 140.8 (14.3)"
[1] "hr=" "1.1"
D44V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q21) MUTATED         0       53        50       75
  DEL PEAK 11(6Q21) WILD-TYPE       4       71        77       54
D44V3, multiclass
           clus
vv          DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  STAGE I                           0                           4
  STAGE II                         53                          71
  STAGE III                        50                          77
  STAGE IV                         75                          54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 11(6Q21) MUTATED         53 92 22
  DEL PEAK 11(6Q21) WILD-TYPE       68 92 31
D44V4, multiclass
          clus
vv         DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        53                          68
  T3                              92                          92
  T4                              22                          31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 11(6Q21) MUTATED    87  21  49   4
  DEL PEAK 11(6Q21) WILD-TYPE 137  21  26   4
D44V5, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  N0                        87                         137
  N1                        21                          21
  N2                        49                          26
  N3                         4                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    80   2
  DEL PEAK 11(6Q21) WILD-TYPE 105   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     80    2
  DEL PEAK 11(6Q21) WILD-TYPE  105    8
   clus
vv  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  0                        80                         105
  1                         2                           8
[1] 2 2
[1] FALSE
D44V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    54 128
  DEL PEAK 11(6Q21) WILD-TYPE  47 160
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     54  128
  DEL PEAK 11(6Q21) WILD-TYPE   47  160
        clus
vv       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  FEMALE                        54                          47
  MALE                         128                         160
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q21) MUTATED      14                        10   148
  DEL PEAK 11(6Q21) WILD-TYPE    28                        11   163
D44V11, multiclass
                           clus
vv                          DEL PEAK 11(6Q21) MUTATED
  ASIAN                                            14
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                           148
                           clus
vv                          DEL PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED     7 162
  DEL PEAK 11(6Q21) WILD-TYPE   2 190
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED      7  162
  DEL PEAK 11(6Q21) WILD-TYPE    2  190
                        clus
vv                       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             7                           2
  NOT HISPANIC OR LATINO                       162                         190
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 12(6Q27) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q27) MUTATED   101  76
  DEL PEAK 12(6Q27) WILD-TYPE 129  77
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        177                         206 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                         76                          77 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q 
       22.29       103.50       105.70         8.35        16.27        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       17.16        27.62         0.62        41.75        51.16        10.22 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       19.04        32.84         5.06        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A0YR 
        9.96        28.70         1.94         0.46        12.62         7.20 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD 
        5.19         1.84        21.86        66.41        16.70       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
       13.58         8.22        17.72        50.27        21.30        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       17.98        64.18        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       13.58       166.03        12.36        10.49         8.65        13.64 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME 
       12.03        43.59        15.35         0.49         0.56        12.99 
TCGA-E7-A7DV TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ 
        1.22        12.95         8.94        23.41        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       19.79        12.85        15.58        26.73        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.36         8.25        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        13.35        62.86         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
        4.31        31.07         6.48        35.24        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD 
       17.62        64.44        19.46         2.24         4.50        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R 
        0.49         8.94         7.73         2.10        10.92        11.31 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        7.63         4.73        32.98         7.00        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
       19.82        20.28         8.48        10.59         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB 
       22.72        19.40        38.60         3.06        25.02         2.76 
TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       27.68        11.70         1.81        15.58        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        65.75       112.83        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        1.64        45.04         6.58        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SW 
        1.87        17.88        48.62        79.66         3.22        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       28.24        26.27         2.24        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 
        8.32         6.77        44.32        56.48        86.30        75.39 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 
       11.97        13.64        18.64         7.36        21.11        21.86 
TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA52 
       28.41         2.89        34.06        19.69        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       57.90        19.40        19.17 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       11.97        91.63        44.94        16.83        34.98        49.12 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        15.12        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.66         6.74        12.39         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16        12.82        17.56        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98        23.01         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.46        16.31        13.58         2.14        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IU 
      130.88        16.14        17.62        15.62         7.82        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81        10.55       140.81        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 
       67.36        15.68         7.53        43.50        10.62        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70        17.39         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       14.56        13.97        14.33         0.92        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       15.32        14.37         8.09        32.02        16.77        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       17.98         5.52        25.74        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TB 
       20.91         3.62        53.88         5.69         2.70        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         2.27         9.67        10.85         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO 
       26.93         7.23        66.02         6.94        21.40        15.81 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75        24.92        13.91         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.20         7.36        11.31        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
       10.65        14.27        27.35         1.51         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
        3.45        21.24         9.14         9.07         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
        6.38        11.80        15.32        21.07        12.23         3.75 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A8HE 
       86.83        76.01        67.79         3.58        35.24       125.49 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 
       64.80        66.41        12.76        23.64        21.04        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAN1 
      110.60        11.31        71.57         2.96        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       61.45        27.06        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD 
        0.66        24.13        30.28        27.19        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.61        59.38        60.16        38.73         8.52        47.15 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                       0.46                        0.10 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     166.03                      140.81 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                      16.77                       15.22 
[1] "0.5 - 166.0 (16.8)" "0.1 - 140.8 (15.2)"
[1] "hr=" "1.1"
D45V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q27) MUTATED         1       48        52       75
  DEL PEAK 12(6Q27) WILD-TYPE       3       76        75       54
D45V3, multiclass
           clus
vv          DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  STAGE I                           1                           3
  STAGE II                         48                          76
  STAGE III                        52                          75
  STAGE IV                         75                          54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 12(6Q27) MUTATED         49 90 24
  DEL PEAK 12(6Q27) WILD-TYPE       72 94 29
D45V4, multiclass
          clus
vv         DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  T0+T1+T2                        49                          72
  T3                              90                          94
  T4                              24                          29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 12(6Q27) MUTATED    87  19  50   4
  DEL PEAK 12(6Q27) WILD-TYPE 137  23  25   4
D45V5, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  N0                        87                         137
  N1                        19                          23
  N2                        50                          25
  N3                         4                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED    79   2
  DEL PEAK 12(6Q27) WILD-TYPE 106   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED     79    2
  DEL PEAK 12(6Q27) WILD-TYPE  106    8
   clus
vv  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  0                        79                         106
  1                         2                           8
[1] 2 2
[1] FALSE
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED    47 132
  DEL PEAK 12(6Q27) WILD-TYPE  54 156
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED     47  132
  DEL PEAK 12(6Q27) WILD-TYPE   54  156
        clus
vv       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  FEMALE                        47                          54
  MALE                         132                         156
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q27) MUTATED      14                        10   146
  DEL PEAK 12(6Q27) WILD-TYPE    28                        11   165
D45V11, multiclass
                           clus
vv                          DEL PEAK 12(6Q27) MUTATED
  ASIAN                                            14
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                           146
                           clus
vv                          DEL PEAK 12(6Q27) WILD-TYPE
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     6 158
  DEL PEAK 12(6Q27) WILD-TYPE   3 194
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      6  158
  DEL PEAK 12(6Q27) WILD-TYPE    3  194
                        clus
vv                       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             6                           3
  NOT HISPANIC OR LATINO                       158                         194
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    38  19
  DEL PEAK 13(7Q36.3) WILD-TYPE 192 134
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           57                           326 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           19                           134 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20X TCGA-CF-A1HS 
        8.35        17.16         2.66        32.84         8.25         0.43 
TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA77 
       12.62       123.85         2.20         7.82        15.02        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A97P TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.35        38.83        12.99        14.37        27.98        60.66 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FD-A6TF 
        8.25        27.45        18.08        62.86        12.36         2.27 
TCGA-FJ-A3ZF TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW 
       17.23         2.24         4.50        14.07        24.92         0.49 
TCGA-GC-A6I1 TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
        8.94         7.63         5.62        10.65        32.98         7.00 
TCGA-GV-A3QI TCGA-K4-A3WS TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-LC-A66R 
       10.59        25.02         9.07        11.70        15.42        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A8OB TCGA-XF-A8HD TCGA-XF-AAMG 
       15.58        12.23        16.67        65.75        97.45       110.60 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RF 
        7.63         2.96        44.32        13.64        74.56        52.73 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4W 
       82.49        47.84        60.16 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        16.77        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        33.83        40.08         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
        5.06        14.89        14.96         5.06         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        24.26        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32        13.58         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        30.67        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       17.39         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.62        22.52        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 
       53.88        11.01        19.33         5.36         5.69        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13        10.65         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 
       21.40        15.81        15.91        17.75        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV 
       11.31        11.31        27.09        20.05         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       21.34        19.10        19.82        20.28         8.48        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01         8.22         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO 
        9.14        27.68         1.74         1.81         6.38        11.80 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        13.48        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       67.79         3.58       112.83        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF 
        4.54         1.64        45.04         6.58       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       71.57        91.73         8.32         6.77        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        13.41         3.48        52.60        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       123.85                        166.03 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       14.370                        16.225 
[1] "0.4 - 123.8 (14.4)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(7Q36.3) MUTATED         0       17        20       19
  DEL PEAK 13(7Q36.3) WILD-TYPE       4      107       107      110
D46V3, multiclass
           clus
vv          DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           17                           107
  STAGE III                          20                           107
  STAGE IV                           19                           110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 13(7Q36.3) MUTATED         15  30   8
  DEL PEAK 13(7Q36.3) WILD-TYPE      106 154  45
D46V4, multiclass
          clus
vv         DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  T0+T1+T2                          15                           106
  T3                                30                           154
  T4                                 8                            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"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 13(7Q36.3) MUTATED    33   4  14   0
  DEL PEAK 13(7Q36.3) WILD-TYPE 191  38  61   8
D46V5, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  N0                          33                           191
  N1                           4                            38
  N2                          14                            61
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    19   1
  DEL PEAK 13(7Q36.3) WILD-TYPE 166   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     19    1
  DEL PEAK 13(7Q36.3) WILD-TYPE  166    9
   clus
vv  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  0                          19                           166
  1                           1                             9
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    13  44
  DEL PEAK 13(7Q36.3) WILD-TYPE  88 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     13   44
  DEL PEAK 13(7Q36.3) WILD-TYPE   88  244
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          13                            88
  MALE                            44                           244
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       4                         2    48
  DEL PEAK 13(7Q36.3) WILD-TYPE    38                        19   263
D46V11, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              48
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED     3  52
  DEL PEAK 13(7Q36.3) WILD-TYPE   6 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED      3   52
  DEL PEAK 13(7Q36.3) WILD-TYPE    6  300
                        clus
vv                       DEL PEAK 13(7Q36.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK 13(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           300
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED   142  84
  DEL PEAK 14(8P23.3) WILD-TYPE  88  69
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          226                           157 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           84                            69 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        16.77        17.16        27.62         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J 
       51.16        10.22        47.80        40.08         2.66        19.04 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         8.35        16.18        12.82         9.96        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C 
       24.26        28.41         8.98         1.94         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
       10.95        11.34        11.87        12.92         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19        21.86         2.14        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       64.18        15.68        41.06        38.24        15.02       166.03 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       10.49         8.65        12.03        10.62        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DU 
       24.66         0.49        17.39         0.56        14.56         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.22        13.68        14.37         8.09        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        22.52        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y 
        5.52        25.74        19.79        22.98        27.35        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       26.73        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        2.70         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.36         2.27         4.31        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE 
       10.65        17.23         6.48        61.94        15.95        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC 
       17.62         6.94        64.44        19.46         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         0.49        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        20.05         5.62         4.73        10.65        32.98 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.10        19.82         8.48         8.58        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         2.76         9.14        27.68         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       15.42         6.38        11.80        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        16.67        14.24        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        65.75         3.58 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
      112.83        29.56        17.82         4.54         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ 
        6.58        15.35         1.87        48.62        79.66         3.22 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG 
       12.76        11.90        26.27         2.24        66.64       110.60 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H 
       98.99        56.48        61.45        75.39        18.81        18.84 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       18.64         7.36        30.28        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       52.73        82.49        20.22        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
        8.52        47.15        19.17        10.13 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA84 
       91.63        44.94        34.98        49.12        66.54        15.12 
TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       33.83         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         8.25        17.16        20.48         4.67        17.56 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       23.01         0.46        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.34        13.08 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA 
        4.90        16.31         1.84        13.58        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IS 
       16.70        16.14        17.62        15.62         7.79        50.27 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.81        10.55       140.81        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       76.60        67.36        30.67        13.58        12.36         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       13.64        43.50        43.59         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
        0.66        13.97        12.99        14.33        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN 
       15.32        32.02        12.62        27.98        60.66        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
       46.78        12.85        14.96        20.91         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TG 
       11.01         5.36        58.92         7.10        18.81         3.06 
TCGA-FD-A6TI TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        9.67         8.94         3.25        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       33.01         7.23        66.02        21.40         2.24        15.81 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV 
        8.94        11.31        11.31        27.09         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE 
       21.34        20.28        10.59        27.35         1.51        38.60 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78P 
        9.07        11.70        12.23         1.84         3.75        67.79 
TCGA-UY-A9PA TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH 
       35.24        97.45       125.49        97.12        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 
       66.41        23.64        21.04        28.24        18.90        16.27 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR 
        2.10        13.74        92.98        10.82        11.31        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        86.30        27.06         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        13.64        21.11        24.13        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA54 
       21.86        28.41        52.60        47.84         2.89        19.40 
TCGA-ZF-AA5N 
        5.52 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        15.63                         15.81 
[1] "0.4 - 166.0 (15.6)" "0.1 - 140.8 (15.8)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.3) MUTATED         3       70        65       86
  DEL PEAK 14(8P23.3) WILD-TYPE       1       54        62       43
D47V3, multiclass
           clus
vv          DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  STAGE I                             3                             1
  STAGE II                           70                            54
  STAGE III                          65                            62
  STAGE IV                           86                            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 14(8P23.3) MUTATED         69 103  34
  DEL PEAK 14(8P23.3) WILD-TYPE       52  81  19
D47V4, multiclass
          clus
vv         DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T0+T1+T2                          69                            52
  T3                               103                            81
  T4                                34                            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(8P23.3) MUTATED   116  31  48   6
  DEL PEAK 14(8P23.3) WILD-TYPE 108  11  27   2
D47V5, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  N0                         116                           108
  N1                          31                            11
  N2                          48                            27
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   99  7
  DEL PEAK 14(8P23.3) WILD-TYPE 86  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     99    7
  DEL PEAK 14(8P23.3) WILD-TYPE   86    3
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                          99                            86
  1                           7                             3
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    57 170
  DEL PEAK 14(8P23.3) WILD-TYPE  44 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     57  170
  DEL PEAK 14(8P23.3) WILD-TYPE   44  118
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          57                            44
  MALE                           170                           118
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED      17                        17   184
  DEL PEAK 14(8P23.3) WILD-TYPE    25                         4   127
D47V11, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                          17
  WHITE                                             184
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     5 204
  DEL PEAK 14(8P23.3) WILD-TYPE   4 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      5  204
  DEL PEAK 14(8P23.3) WILD-TYPE    4  148
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         204
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           148
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 15(8P21.3) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P21.3) MUTATED   150  86
  DEL PEAK 15(8P21.3) WILD-TYPE  80  67
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          236                           147 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                           86                            67 
$`DEL PEAK 15(8P21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.77        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J 
       15.12        10.22        47.80        33.83        40.08         2.66 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
       19.04         5.06         8.35        16.18        20.48        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        28.70        24.26        28.41         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
        0.43         0.69        10.95        11.34        11.34        11.87 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.92         5.46         5.19        16.31        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       18.41       130.88       112.44         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       21.30        23.21         9.67        64.18        15.68        41.06 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 
       38.24        15.02       166.03        10.49         8.65        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       10.62        15.35        38.83        24.66         0.49        17.39 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
        0.56        14.56         0.92         1.22        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37         8.09        16.77         8.94        33.04         4.01 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85        22.98        27.35 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       15.58        26.73        19.33         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       18.08         2.70         6.28        13.35        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69        12.36         2.27         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
        7.13        10.65        17.23         6.48        61.94        15.95 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        4.50        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10         3.12         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         7.63        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        19.07        22.72        19.40         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67        14.24         1.84        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        76.01        65.75         3.58       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         4.54         1.64        45.04         6.58 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV 
       15.35         1.87        48.62        79.66         3.22        12.76 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ 
       11.90        26.27         2.24        66.64       110.60        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57         2.96         8.32         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       56.48        61.45        75.39        18.84        18.64         7.36 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       30.28        21.86        13.41         3.48        52.73        82.49 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        35.41        57.90         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

$`DEL PEAK 15(8P21.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       91.63        44.94        16.83        34.98        49.12        66.54 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         6.74        12.39         6.58        13.15        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.25        17.16         4.67        17.56        23.01         0.46 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 
       12.00        12.10        13.08         4.90         7.20         1.84 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58        66.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       15.62         7.79        50.27        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       48.00        17.98        41.56        76.60        67.36        30.67 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC 
       13.58        12.36         7.53        13.64        43.50        43.59 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME 
        0.10         2.24        16.70         0.66        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.33        14.07        15.32        32.02        12.62        27.98 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TI 
        5.36        58.92         7.10        18.81         3.06         9.67 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        8.94         3.25        30.61        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS 
        7.23        21.40         2.24        15.81         8.94        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI 
        2.20        11.31        27.09         7.00        14.27        10.59 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A5RI TCGA-S5-AA26 TCGA-UY-A78N 
       27.35         1.51        38.60        11.70         3.75        86.83 
TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
       67.79        35.24        97.45       125.49        97.12        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       64.80        66.41        23.64        21.04        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       16.27         2.10        13.74        92.98        10.82        11.31 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
       91.73        44.32        30.94        86.30        27.06        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 
        3.88         9.63         0.66        11.97        13.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RG TCGA-ZF-A9RM 
       24.13        27.19        28.41        74.56        52.60        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA54 TCGA-ZF-AA5N 
        2.89        19.40         5.52 

  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                         0.43                          0.10 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                        15.58                         16.14 
[1] "0.4 - 166.0 (15.6)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1.2"
D48V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(8P21.3) MUTATED         3       75        67       90
  DEL PEAK 15(8P21.3) WILD-TYPE       1       49        60       39
D48V3, multiclass
           clus
vv          DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  STAGE I                             3                             1
  STAGE II                           75                            49
  STAGE III                          67                            60
  STAGE IV                           90                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 15(8P21.3) MUTATED         72 106  39
  DEL PEAK 15(8P21.3) WILD-TYPE       49  78  14
D48V4, multiclass
          clus
vv         DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  T0+T1+T2                          72                            49
  T3                               106                            78
  T4                                39                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(8P21.3) MUTATED   123  30  51   7
  DEL PEAK 15(8P21.3) WILD-TYPE 101  12  24   1
D48V5, multiclass
    clus
vv   DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  N0                         123                           101
  N1                          30                            12
  N2                          51                            24
  N3                           7                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED   105   8
  DEL PEAK 15(8P21.3) WILD-TYPE  80   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED    105    8
  DEL PEAK 15(8P21.3) WILD-TYPE   80    2
   clus
vv  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  0                         105                            80
  1                           8                             2
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED    59 179
  DEL PEAK 15(8P21.3) WILD-TYPE  42 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED     59  179
  DEL PEAK 15(8P21.3) WILD-TYPE   42  109
        clus
vv       DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  FEMALE                          59                            42
  MALE                           179                           109
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P21.3) MUTATED      20                        16   193
  DEL PEAK 15(8P21.3) WILD-TYPE    22                         5   118
D48V11, multiclass
                           clus
vv                          DEL PEAK 15(8P21.3) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             193
                           clus
vv                          DEL PEAK 15(8P21.3) WILD-TYPE
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED     6 213
  DEL PEAK 15(8P21.3) WILD-TYPE   3 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED      6  213
  DEL PEAK 15(8P21.3) WILD-TYPE    3  139
                        clus
vv                       DEL PEAK 15(8P21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         213
                        clus
vv                       DEL PEAK 15(8P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           139
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 16(9P23) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(9P23) MUTATED    99  62
  DEL PEAK 16(9P23) WILD-TYPE 131  91
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        161                         222 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                         62                          91 
$`DEL PEAK 16(9P23) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J 
       16.83        34.98        49.12         0.62        40.08         2.66 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
       13.15        19.04        32.84        19.50        14.89         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 
       17.16        16.18         9.96        28.70        24.26         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY 
        0.46         0.69        12.62        13.12        12.00        11.34 
TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       11.87         4.90         5.46        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       21.86        19.00        16.70        17.62        15.62        10.59 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX 
        2.20         8.22        17.72        50.27        21.30        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       48.00        17.98        64.18        15.68        41.06        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        10.49         8.65         7.53        13.64 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 
       12.03        10.62        43.59        38.83        24.66        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B4 
        0.56         0.66         0.92        13.68         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        8.94        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       22.98        26.73         5.36        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG 
        7.10         6.28        13.35        62.86        18.81         3.06 
TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB 
       10.85        10.65         6.48        30.61        35.24         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A3YS 
       17.62        66.02        64.44        19.46        14.07        24.92 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        8.94         3.12        20.98         2.20         7.36        11.31 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW 
        7.63         4.73        10.65        32.98         7.00        21.34 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        27.35        22.72        19.40        38.60         3.06 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI 
       25.02         3.45        21.24         2.76         9.07        11.70 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.42        11.80        21.07        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PE 
        1.84         3.75        31.56        65.75       112.83         4.54 
TCGA-XF-A8HI TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ 
       17.88        12.76        11.90        26.27        16.27        71.57 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 
       91.73         6.77        98.99        44.32        30.94        18.81 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       11.97         7.36        21.11        28.41        74.56         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       82.49         8.61        38.73        19.40         8.52 

$`DEL PEAK 16(9P23) WILD-TYPE`
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 
       22.29        44.94        16.77        17.16        27.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74        12.39         6.58        12.16        17.88 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96         5.06         8.25        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       12.82        17.56        28.41         8.98        23.01         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A7I0 
       10.95        12.66        12.46        12.10        12.26        12.10 
TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 
       11.34        13.08        12.92         7.20         5.19         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX 
       66.41        18.41       130.88       112.44        16.14         1.81 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU 
        7.79       123.85        87.32        13.58         7.82        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        20.81       140.81        41.56        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 
       30.67        38.24        12.36        43.50        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.49         2.24        16.70        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         1.22        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P 
       60.66        24.30        23.41         5.52        25.74        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD 
       19.33         5.69         8.25         2.70         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.36         2.27         4.31         9.67        31.07         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         8.94         3.25        61.94        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       33.01        20.12         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
        4.50        15.91        17.75         0.49        13.91         7.73 
TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.10        10.92        11.31        27.09        20.05         5.62 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
       14.27        19.10        19.82        20.28        10.59         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R 
       19.07         1.51         9.01         8.22         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         1.81         6.38        15.32        15.58        13.48 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       67.79         3.58        35.24        29.56        17.82         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        97.45       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       23.64        21.04        28.24        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 
       54.90         7.63         2.96         8.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        13.64        18.64        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        13.41        52.73        52.60        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        57.90        47.15        19.17         5.52        10.13 

  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                       0.46                        0.10 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     166.03                      140.81 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     15.680                      15.695 
[1] "0.5 - 166.0 (15.7)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1"  
D49V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P23) MUTATED         2       54        57       50
  DEL PEAK 16(9P23) WILD-TYPE       2       70        70       79
D49V3, multiclass
           clus
vv          DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  STAGE I                           2                           2
  STAGE II                         54                          70
  STAGE III                        57                          70
  STAGE IV                         50                          79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2  T3  T4
  DEL PEAK 16(9P23) MUTATED         51  78  23
  DEL PEAK 16(9P23) WILD-TYPE       70 106  30
D49V4, multiclass
          clus
vv         DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  T0+T1+T2                        51                          70
  T3                              78                         106
  T4                              23                          30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 16(9P23) MUTATED   102  14  33   3
  DEL PEAK 16(9P23) WILD-TYPE 122  28  42   5
D49V5, multiclass
    clus
vv   DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  N0                       102                         122
  N1                        14                          28
  N2                        33                          42
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    83   4
  DEL PEAK 16(9P23) WILD-TYPE 102   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     83    4
  DEL PEAK 16(9P23) WILD-TYPE  102    6
   clus
vv  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  0                        83                         102
  1                         4                           6
[1] 2 2
[1] FALSE
D49V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    44 122
  DEL PEAK 16(9P23) WILD-TYPE  57 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     44  122
  DEL PEAK 16(9P23) WILD-TYPE   57  166
        clus
vv       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  FEMALE                        44                          57
  MALE                         122                         166
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P23) MUTATED      17                        10   131
  DEL PEAK 16(9P23) WILD-TYPE    25                        11   180
D49V11, multiclass
                           clus
vv                          DEL PEAK 16(9P23) MUTATED
  ASIAN                                            17
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                           131
                           clus
vv                          DEL PEAK 16(9P23) WILD-TYPE
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED     4 152
  DEL PEAK 16(9P23) WILD-TYPE   5 200
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED      4  152
  DEL PEAK 16(9P23) WILD-TYPE    5  200
                        clus
vv                       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           5
  NOT HISPANIC OR LATINO                       152                         200
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 17(9P21.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9P21.3) MUTATED   132  89
  DEL PEAK 17(9P21.3) WILD-TYPE  98  64
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          221                           162 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                           89                            64 
$`DEL PEAK 17(9P21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.27        16.83        34.98        27.62        49.12         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
       51.16        33.83        40.08         7.33         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        32.84        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35         8.25        16.18 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 
        9.96        17.56        28.70        24.26         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA 
        0.46         0.69        12.66        12.62        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3KJ 
       12.10        11.34        11.34        11.87         4.90         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
       16.31         1.84        13.58        21.86         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK 
       16.70        16.14        17.62        15.62        10.59         2.20 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        17.72        50.27        21.30        20.81        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       48.00        17.98        64.18        15.68        41.06        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        10.49         8.65         7.53        13.64 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 
       12.03        10.62        43.59        38.83        24.66        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H 
        0.56         0.66        14.56         0.92        13.68        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.32        14.37         8.09         8.94        27.98        60.66 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       17.98        29.16        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU 
       22.98        20.91         3.62        15.58        26.73        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.36         5.69        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28        13.35        62.86        18.81        12.69         3.06 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF 
       10.85        31.07        10.65         8.94         6.48        61.94 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       64.44        19.46        21.40        14.07        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
       13.91         3.12        20.98         2.20         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       11.31         7.63        27.09         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        7.00        21.34        20.28         8.48        27.35         8.58 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       22.72        19.40        38.60         3.06         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14         9.07        11.70 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.42        11.80        21.07        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB 
        1.84         3.75        31.56        22.68        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HE TCGA-XF-A8HF 
        3.58       112.83        17.82         4.54       125.49        97.12 
TCGA-XF-A8HI TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 
       17.88        12.76        11.90        26.27        66.64        13.74 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A9TC 
       44.32        30.94        86.30        75.39        18.81         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R7 
       11.97        18.64         7.36        21.11        24.13        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U 
       28.41        74.56         3.48        82.49        20.22         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        57.90        19.40         8.52 

$`DEL PEAK 17(9P21.3) WILD-TYPE`
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       44.94        16.77        17.16        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A2LA 
       10.22        47.80         6.74        12.16         5.06        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS 
       20.48         4.67        12.82        28.41         8.98         0.43 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A9FM TCGA-CU-A0YN 
       10.95        12.46        12.10        12.26        13.08        12.92 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        7.20         5.19        66.41        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81         7.79       123.85        87.32        13.58         7.82 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       23.21         9.67       140.81        41.56        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 
       30.67        38.24        12.36        43.50        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.49         2.24        16.70        13.97        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        14.07        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43P 
       12.62        22.52        24.30        23.41         5.52        27.35 
TCGA-FD-A43S TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC 
       14.96        53.88        11.01         8.25         2.70         6.15 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       12.36         2.27         4.31         9.67         7.13        17.23 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-GC-A3I6 
        3.25        30.61        15.95        26.93        33.01         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 
       15.81         4.50        15.91        17.75         0.49         7.73 
TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX 
        2.10        10.92        20.05         5.62        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A54R 
       19.82        10.59        19.07         1.51         8.22        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         1.81         6.38        15.32        15.58        13.48 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA 
       12.43        17.62        37.05        86.83        76.01        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG 
       29.56         1.64        45.04         6.58        97.45        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
        7.63        56.48        61.45        27.06         3.88        18.84 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF 
        9.63        13.64        30.28        27.19        13.41        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       52.60        47.84         2.89        34.06        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       63.02        35.41        47.15        19.17         5.52        10.13 

  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                         0.46                          0.10 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       15.680                        15.695 
[1] "0.5 - 166.0 (15.7)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(9P21.3) MUTATED         2       74        77       70
  DEL PEAK 17(9P21.3) WILD-TYPE       2       50        50       59
D50V3, multiclass
           clus
vv          DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  STAGE I                             2                             2
  STAGE II                           74                            50
  STAGE III                          77                            50
  STAGE IV                           70                            59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 17(9P21.3) MUTATED         70 105  33
  DEL PEAK 17(9P21.3) WILD-TYPE       51  79  20
D50V4, multiclass
          clus
vv         DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  T0+T1+T2                          70                            51
  T3                               105                            79
  T4                                33                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(9P21.3) MUTATED   135  22  42   3
  DEL PEAK 17(9P21.3) WILD-TYPE  89  20  33   5
D50V5, multiclass
    clus
vv   DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  N0                         135                            89
  N1                          22                            20
  N2                          42                            33
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED   112   5
  DEL PEAK 17(9P21.3) WILD-TYPE  73   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED    112    5
  DEL PEAK 17(9P21.3) WILD-TYPE   73    5
   clus
vv  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  0                         112                            73
  1                           5                             5
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    62 164
  DEL PEAK 17(9P21.3) WILD-TYPE  39 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     62  164
  DEL PEAK 17(9P21.3) WILD-TYPE   39  124
        clus
vv       DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  FEMALE                          62                            39
  MALE                           164                           124
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P21.3) MUTATED      25                        14   177
  DEL PEAK 17(9P21.3) WILD-TYPE    17                         7   134
D50V11, multiclass
                           clus
vv                          DEL PEAK 17(9P21.3) MUTATED
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             177
                           clus
vv                          DEL PEAK 17(9P21.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED     4 207
  DEL PEAK 17(9P21.3) WILD-TYPE   5 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED      4  207
  DEL PEAK 17(9P21.3) WILD-TYPE    5  145
                        clus
vv                       DEL PEAK 17(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         207
                        clus
vv                       DEL PEAK 17(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           145
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 18(9Q22.33) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(9Q22.33) MUTATED   104  59
  DEL PEAK 18(9Q22.33) WILD-TYPE 126  94
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           163                            220 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                            59                             94 
$`DEL PEAK 18(9Q22.33) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.27        16.83        17.16        34.98        49.12         0.62 
TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
       66.54        33.83         6.58        32.84        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F6 TCGA-CF-A1HR 
       14.89        16.18        20.48        28.70        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX 
        0.69        10.95        12.46        12.62        13.12        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        13.08         4.90         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AD 
        1.84        13.58         2.14        66.41        19.00       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX 
       17.62        15.62        17.72        50.27        21.30        10.55 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W 
       17.98        64.18        41.06        15.02        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
        7.53        12.03        10.62        43.59        38.83        24.66 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DU TCGA-E7-A7DV 
       16.70        17.39         0.56         0.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SM 
       13.68         8.09         8.94        33.04         4.01        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        22.98         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       26.73        19.33        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3Z7 
        6.28        62.86        18.81         2.27         3.06        31.07 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
        6.48        15.95        26.93        35.24        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       66.02        19.46        21.40        14.07         0.49         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
        7.73         2.10         2.20        27.09         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
       32.98        14.27        21.34         8.48        27.35        19.07 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       22.72        38.60         3.06         3.45        21.24         2.76 
TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X 
       27.68        11.70        11.80        21.07        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PD 
        1.84         3.75        12.43        31.56        76.01        17.82 
TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SV 
        1.64        97.12        15.35        17.88        64.80        12.76 
TCGA-XF-A9T0 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 
       26.27        71.57        91.73         8.32        44.32        30.94 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.81        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       21.11        24.13        21.86        28.41        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA54 
       52.73        82.49        20.22         8.61        38.73        19.40 
TCGA-ZF-AA58 
       47.15 

$`DEL PEAK 18(9Q22.33) WILD-TYPE`
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       44.94        16.77        27.62        41.75        51.16        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U 
       12.39        13.15        19.04        12.16         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        24.26        28.41         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
        0.43        12.66        12.10        12.26        12.00        12.10 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AB 
       12.92         7.20        16.31        21.86        18.41        16.70 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88        16.14         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
       87.32         2.20        13.58         7.82         8.22        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81       140.81        48.00        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S 
       67.36        15.68        30.67        38.24        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.36        13.64        43.50        15.35         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        2.24        14.56        13.97        12.99        14.33        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.95        15.32        14.37        32.02        16.77        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        23.41        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS 
        5.52        25.74        27.35        14.96        20.91        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S 
       11.01         5.36         5.69         8.25         2.70        13.35 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69        12.36         4.31         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        7.13        10.65        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 
       30.61        33.01         7.23         6.94        64.44         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 
       15.81         4.50        15.91        17.75        24.92        13.91 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.63        20.05         5.62         7.00        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND 
       20.28        10.59         8.58         1.51        19.40         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.22        25.02         9.14         9.07         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       15.42         6.38        15.32        15.58        13.48        12.23 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB 
        3.58       112.83        35.24        29.56         4.54        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
        6.58        97.45       125.49         1.87        48.62        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96         6.77        98.99        56.48        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R4 
       27.06         3.88        18.84         9.63         0.66        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       27.19        13.41        52.60        47.84         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
       19.69        59.38        60.16        63.02        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        19.17         5.52        10.13 

  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                          0.46                           0.10 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                        112.44                         166.03 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                         17.62                          14.76 
[1] "0.5 - 112.4 (17.6)" "0.1 - 166.0 (14.8)"
[1] "hr=" "1.2"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(9Q22.33) MUTATED         2       61        51       50
  DEL PEAK 18(9Q22.33) WILD-TYPE       2       63        76       79
D51V3, multiclass
           clus
vv          DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            61                             63
  STAGE III                           51                             76
  STAGE IV                            50                             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 18(9Q22.33) MUTATED         58  72  24
  DEL PEAK 18(9Q22.33) WILD-TYPE       63 112  29
D51V4, multiclass
          clus
vv         DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  T0+T1+T2                           58                             63
  T3                                 72                            112
  T4                                 24                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 18(9Q22.33) MUTATED   101  13  32   3
  DEL PEAK 18(9Q22.33) WILD-TYPE 123  29  43   5
D51V5, multiclass
    clus
vv   DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  N0                          101                            123
  N1                           13                             29
  N2                           32                             43
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(9Q22.33) MUTATED   89  3
  DEL PEAK 18(9Q22.33) WILD-TYPE 96  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED     89    3
  DEL PEAK 18(9Q22.33) WILD-TYPE   96    7
   clus
vv  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  0                           89                             96
  1                            3                              7
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED    45 122
  DEL PEAK 18(9Q22.33) WILD-TYPE  56 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED     45  122
  DEL PEAK 18(9Q22.33) WILD-TYPE   56  166
        clus
vv       DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  FEMALE                           45                             56
  MALE                            122                            166
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9Q22.33) MUTATED      20                         7   131
  DEL PEAK 18(9Q22.33) WILD-TYPE    22                        14   180
D51V11, multiclass
                           clus
vv                          DEL PEAK 18(9Q22.33) MUTATED
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              131
                           clus
vv                          DEL PEAK 18(9Q22.33) WILD-TYPE
  ASIAN                                                 22
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED     3 149
  DEL PEAK 18(9Q22.33) WILD-TYPE   6 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED      3  149
  DEL PEAK 18(9Q22.33) WILD-TYPE    6  203
                        clus
vv                       DEL PEAK 18(9Q22.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 18(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 19(10P11.21) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10P11.21) MUTATED    41  29
  DEL PEAK 19(10P11.21) WILD-TYPE 189 124
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             70                             313 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             29                             124 
$`DEL PEAK 19(10P11.21) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-BT-A20J TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42C 
      103.50        16.77        19.04        14.96        17.16        28.70 
TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 
        1.94         0.69        11.34         7.20         5.46         1.84 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-AA6L 
        1.81         7.79         2.20        50.27        21.30        38.24 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        10.49         8.65         7.53        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.35        17.39         1.22        16.77         8.94         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD 
       22.52        19.79        12.85        15.58         8.25        12.69 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3D 
       31.07        10.65        17.23        26.93         7.23        64.44 
TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GV-A40G TCGA-H4-A2HQ 
       21.40        15.91        17.75        13.91        19.07        19.40 
TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A9PB 
        3.45         9.07        11.70        13.48        12.23        29.56 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
        4.54         6.58       125.49         1.87        48.62        79.66 
TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       12.76        10.82         6.77         7.36        13.41         3.48 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA56 
       47.84         2.89        60.16         8.52 

$`DEL PEAK 19(10P11.21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       24.26        28.41         8.98        23.01         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
       12.92         4.90         5.19        16.31        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
       87.32        13.58         7.82         8.22        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 
       30.67        13.58       166.03        12.36        13.64        43.50 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       14.33         0.92        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.37         8.09        32.02        33.04        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.27         3.06         4.31         9.67        10.85         7.13 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25         6.48        61.94        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS 
       19.46         2.24        15.81         4.50        14.07        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49         8.94         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22        25.02        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.14        27.68         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN 
        6.38        11.80        15.32        15.58        21.07        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       37.05        22.68        86.83        76.01        67.79        65.75 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
        3.58       112.83        35.24        17.82         1.64        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SJ 
       97.45        97.12        15.35        17.88        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
       28.41        74.56        52.73        52.60        82.49        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        57.90        19.40        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                           0.69                            0.10 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                         125.49                          166.03 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                          13.13                           16.31 
[1] "0.7 - 125.5 (13.1)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.3"
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(10P11.21) MUTATED         1       22        23       22
  DEL PEAK 19(10P11.21) WILD-TYPE       3      102       104      107
D52V3, multiclass
           clus
vv          DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  STAGE I                               1                               3
  STAGE II                             22                             102
  STAGE III                            23                             104
  STAGE IV                             22                             107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  DEL PEAK 19(10P11.21) MUTATED         18  28  12
  DEL PEAK 19(10P11.21) WILD-TYPE      103 156  41
D52V4, multiclass
          clus
vv         DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  T0+T1+T2                            18                             103
  T3                                  28                             156
  T4                                  12                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 19(10P11.21) MUTATED    43   5  13   4
  DEL PEAK 19(10P11.21) WILD-TYPE 181  37  62   4
D52V5, multiclass
    clus
vv   DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  N0                            43                             181
  N1                             5                              37
  N2                            13                              62
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    29   3
  DEL PEAK 19(10P11.21) WILD-TYPE 156   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     29    3
  DEL PEAK 19(10P11.21) WILD-TYPE  156    7
   clus
vv  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  0                            29                             156
  1                             3                               7
[1] 2 2
[1] FALSE
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    19  51
  DEL PEAK 19(10P11.21) WILD-TYPE  82 237
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     19   51
  DEL PEAK 19(10P11.21) WILD-TYPE   82  237
        clus
vv       DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  FEMALE                            19                              82
  MALE                              51                             237
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10P11.21) MUTATED       4                         8    55
  DEL PEAK 19(10P11.21) WILD-TYPE    38                        13   256
D52V11, multiclass
                           clus
vv                          DEL PEAK 19(10P11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                55
                           clus
vv                          DEL PEAK 19(10P11.21) WILD-TYPE
  ASIAN                                                  38
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED     1  66
  DEL PEAK 19(10P11.21) WILD-TYPE   8 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED      1   66
  DEL PEAK 19(10P11.21) WILD-TYPE    8  286
                        clus
vv                       DEL PEAK 19(10P11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            66
                        clus
vv                       DEL PEAK 19(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             286
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 20(10Q23.31) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10Q23.31) MUTATED    90  66
  DEL PEAK 20(10Q23.31) WILD-TYPE 140  87
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            156                             227 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                             66                              87 
$`DEL PEAK 20(10Q23.31) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       22.29        11.97       103.50        16.27        16.77        17.16 
TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       51.16        15.12        32.84         5.06        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
        8.35        20.48        17.56         1.94        23.01         0.69 
TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 
       11.34         4.90         5.46         5.19         1.84         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       18.41       112.44         1.81         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6B1 
       13.58         7.82         8.22        50.27         9.67        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       30.67        38.24        15.02       166.03        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
        7.53        12.03        43.59        24.66         0.49        17.39 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.99         1.22        13.68        15.32        33.04         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       22.52        24.30        19.79        12.85        22.98        27.35 
TCGA-FD-A43U TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TD 
       20.91         8.25        27.45        58.92        62.86        12.69 
TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EK 
        2.27        31.07        10.65        17.23         6.48        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       19.46        21.40        15.91        14.07        17.75         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 
        8.94        13.91         2.10         7.36        10.92        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73         7.00        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF 
        8.48        10.59        19.07        22.72        19.40         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        9.01        25.02         3.45         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
       11.70         1.74         1.81        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PD 
       13.48        12.23        31.56        76.01        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        4.54         6.58        97.45       125.49        97.12         1.87 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9T8 
       48.62        79.66         3.22        12.76        23.64        13.74 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       10.82        54.90         7.63         2.96         8.32         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       44.32        61.45        18.81        11.97        13.64        18.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.11        74.56         3.48        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        19.69         8.61        63.02        38.73        35.41 

$`DEL PEAK 20(10Q23.31) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       91.63       105.70         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        49.12         0.62        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50        14.89         8.25        17.16        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        28.70        24.26        28.41         8.98 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.43        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E 
       11.87        13.08        12.92         7.20        16.31        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       21.86        66.41        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IT 
       17.62        15.62        10.59       123.85        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q 
       64.18        41.56        76.60        15.68        41.06        13.58 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       12.36        13.64        43.50        10.62        15.35        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       13.97        14.33         0.92        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
        8.09        32.02        16.77         8.94        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N 
       11.01        19.33         5.36         5.69        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        7.10         6.28        13.35        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        3.06         4.31         9.67        10.85         7.13         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3D 
        3.25        61.94        30.61        35.24        33.01        64.44 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ 
        2.24        15.81         4.50        24.92         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        11.31        11.31         7.63        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QK TCGA-GV-A40E 
        5.62        10.65        32.98        14.27        27.35         8.58 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
        1.51        38.60         8.22        21.24         2.76        15.42 
TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
        6.38        21.07        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       12.43        17.62        37.05        22.68        86.83        67.79 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       65.75         3.58       112.83        29.56         1.64        45.04 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SY 
       15.35        17.88        64.80        66.41        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        92.98       110.60        11.31        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        56.48        30.94        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        3.88        18.84         9.63         0.66         7.36        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       30.28        27.19        21.86        28.41        13.41        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 
       52.60        82.49        59.38        60.16        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                           0.49                            0.10 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         166.03                          140.81 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                          15.32                           16.14 
[1] "0.5 - 166.0 (15.3)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1.2"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(10Q23.31) MUTATED         1       53        46       54
  DEL PEAK 20(10Q23.31) WILD-TYPE       3       71        81       75
D53V3, multiclass
           clus
vv          DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  STAGE I                               1                               3
  STAGE II                             53                              71
  STAGE III                            46                              81
  STAGE IV                             54                              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  DEL PEAK 20(10Q23.31) MUTATED         46  74  18
  DEL PEAK 20(10Q23.31) WILD-TYPE       75 110  35
D53V4, multiclass
          clus
vv         DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  T0+T1+T2                            46                              75
  T3                                  74                             110
  T4                                  18                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 20(10Q23.31) MUTATED    81  17  30   5
  DEL PEAK 20(10Q23.31) WILD-TYPE 143  25  45   3
D53V5, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  N0                            81                             143
  N1                            17                              25
  N2                            30                              45
  N3                             5                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    65   5
  DEL PEAK 20(10Q23.31) WILD-TYPE 120   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     65    5
  DEL PEAK 20(10Q23.31) WILD-TYPE  120    5
   clus
vv  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  0                            65                             120
  1                             5                               5
[1] 2 2
[1] FALSE
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    40 116
  DEL PEAK 20(10Q23.31) WILD-TYPE  61 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     40  116
  DEL PEAK 20(10Q23.31) WILD-TYPE   61  172
        clus
vv       DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  FEMALE                            40                              61
  MALE                             116                             172
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q23.31) MUTATED      10                        10   127
  DEL PEAK 20(10Q23.31) WILD-TYPE    32                        11   184
D53V11, multiclass
                           clus
vv                          DEL PEAK 20(10Q23.31) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               127
                           clus
vv                          DEL PEAK 20(10Q23.31) WILD-TYPE
  ASIAN                                                  32
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED     3 141
  DEL PEAK 20(10Q23.31) WILD-TYPE   6 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED      3  141
  DEL PEAK 20(10Q23.31) WILD-TYPE    6  211
                        clus
vv                       DEL PEAK 20(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           141
                        clus
vv                       DEL PEAK 20(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             211
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11P15.5) MUTATED   115  78
  DEL PEAK 21(11P15.5) WILD-TYPE 115  75
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           193                            190 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            78                             75 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       22.29       103.50       105.70         8.35        16.83        16.77 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 
       34.98        27.62         0.62        15.12        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       40.08         2.66        19.04        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.35         4.67         9.96        17.56        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY 
       10.95        12.62        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       11.87         7.20         5.46         1.84        13.58         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41        16.70       112.44        17.62         1.81        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6L 
       50.27        21.30        17.98        64.18        41.06        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       15.02       166.03        10.49        43.50        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       15.35        38.83        24.66        17.39         0.56         0.66 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
       12.99         0.92         1.22        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        8.09         8.94         4.01        24.30        23.41        29.16 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79        12.85        22.98        15.58         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        6.15         2.27         3.06         4.31        31.07        10.65 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
        6.48        35.24        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 
       19.46        21.40         2.24        14.07        24.92         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 
        2.10         2.20         7.36        11.31        11.31         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E 
       32.98         7.00        14.27        21.34        20.28         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72        19.40        38.60         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A8JT 
       25.02        21.24        11.70        15.42        11.80        21.07 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD 
       22.68        76.01        65.75         3.58       112.83        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64        97.12        15.35        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-A9T5 
        3.22        12.76        11.90        28.24         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10       110.60        54.90         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L 
        8.32         6.77        44.32        56.48        18.81        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       18.64         7.36        21.11        30.28        21.86        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       34.06        19.69         8.61        63.02        35.41        19.17 
TCGA-ZF-AA5P 
       10.13 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7Y 
       11.97        91.63        16.27        44.94        17.16        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A3JM 
       41.75        51.16        66.54        10.22         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
       14.96         8.25        17.16        16.18        20.48        12.82 
TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       24.26        28.41        12.66        12.46        12.10        12.26 
TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        13.08        12.92         4.90         5.19        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG 
       21.86        66.41        19.00       130.88        16.14        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.79       123.85        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      140.81        48.00        41.56        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       30.67        13.58        12.36         8.65         7.53        13.64 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 
       43.59         0.10         0.49         2.24        16.70        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.97        14.33        14.07        15.32        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM 
       33.04        12.62        22.52        27.98        60.66        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        25.74        46.78        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI 
        8.25        13.35        18.81        12.69        12.36         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85         7.13        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C 
       30.61        15.95        26.93        33.01         7.23         6.94 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81         4.50        15.91        17.75         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 
       13.91         3.12        20.98        10.92         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
       20.05         5.62        10.65        19.10        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
       10.59        27.35         1.51         8.22         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        9.14        27.68         9.07         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L 
       15.32        15.58        13.48        16.67        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC 
       86.83        67.79        35.24        29.56        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SL 
       97.45       125.49         1.87        17.88        79.66        66.41 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T8 
       23.64        21.04        26.27        18.90        16.27        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAN1 
       92.98        10.82        11.31         2.96        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        9.63         0.66        13.64        24.13        27.19        28.41 
TCGA-ZF-A9RF TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 
       52.73         2.89        59.38        60.16        38.73        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       19.40         8.52        47.15         5.52 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        166.03                         140.81 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                         15.12                          16.16 
[1] "0.4 - 166.0 (15.1)" "0.1 - 140.8 (16.2)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(11P15.5) MUTATED         2       61        54       76
  DEL PEAK 21(11P15.5) WILD-TYPE       2       63        73       53
D54V3, multiclass
           clus
vv          DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            61                             63
  STAGE III                           54                             73
  STAGE IV                            76                             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 21(11P15.5) MUTATED         63 94 29
  DEL PEAK 21(11P15.5) WILD-TYPE       58 90 24
D54V4, multiclass
          clus
vv         DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  T0+T1+T2                           63                             58
  T3                                 94                             90
  T4                                 29                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 21(11P15.5) MUTATED   103  21  50   4
  DEL PEAK 21(11P15.5) WILD-TYPE 121  21  25   4
D54V5, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  N0                          103                            121
  N1                           21                             21
  N2                           50                             25
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED   98  7
  DEL PEAK 21(11P15.5) WILD-TYPE 87  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     98    7
  DEL PEAK 21(11P15.5) WILD-TYPE   87    3
   clus
vv  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  0                           98                             87
  1                            7                              3
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED    51 147
  DEL PEAK 21(11P15.5) WILD-TYPE  50 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     51  147
  DEL PEAK 21(11P15.5) WILD-TYPE   50  141
        clus
vv       DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  FEMALE                           51                             50
  MALE                            147                            141
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED      27                        10   150
  DEL PEAK 21(11P15.5) WILD-TYPE    15                        11   161
D54V11, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              150
                           clus
vv                          DEL PEAK 21(11P15.5) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED     6 175
  DEL PEAK 21(11P15.5) WILD-TYPE   3 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      6  175
  DEL PEAK 21(11P15.5) WILD-TYPE    3  177
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            177
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 22(11Q23.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11Q23.3) MUTATED    84  59
  DEL PEAK 22(11Q23.3) WILD-TYPE 146  94
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           143                            240 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                            59                             94 
$`DEL PEAK 22(11Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       22.29       103.50       105.70        16.83        34.98         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T 
       41.75        51.16        33.83        19.04        32.84        14.89 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        8.35        17.16        16.18         4.67        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A5U8 
       28.41         8.98         0.43         0.69        12.62        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 
       12.10        11.34        11.34        12.92         5.46         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A3IM TCGA-DK-A3IN 
       66.41        16.70       130.88       112.44         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       17.72        50.27        64.18        30.67        15.02       166.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       43.59        15.35        38.83         0.49        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.66        12.99         0.92        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43X 
        8.09         8.94         4.01        24.30        22.98         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       15.58        26.73         5.36         8.25        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH 
        2.70         7.10        13.35        62.86         6.15         4.31 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3YS 
        6.48        33.01         7.23        64.44        21.40        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q 
        0.49         8.94         7.73         2.10         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK 
       11.31         4.73         7.00        14.27        21.34        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72        19.40        38.60         3.06 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-PQ-A6FI 
       21.24         2.76         9.14         9.07        11.70        12.23 
TCGA-SY-A9G5 TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       31.56        86.83        76.01        67.79        65.75         3.58 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SV 
      112.83        29.56         4.54        15.35        48.62        12.76 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ 
       11.90        66.64         2.10        10.82       110.60        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
        7.63        71.57         2.96         8.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       61.45        18.81        18.64        21.11        30.28        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       74.56        13.41        20.22        19.69         8.61        63.02 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40        47.15        19.17        10.13 

$`DEL PEAK 22(11Q23.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        91.63         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       17.16        27.62        49.12        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        13.15        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         5.06         8.25        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T 
       24.26         1.94        23.01         0.46        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A9FF TCGA-CF-A9FM 
       12.46        12.10        12.26        12.00        11.87        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        18.41        19.00        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       13.58        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        41.06        38.24        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 
       24.66         0.10         2.24        16.70        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.33         1.22        14.07        15.32        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
       33.04        12.62        22.52        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35        14.96        20.91        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD 
       19.33         5.69        27.45         6.28        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        7.13        10.65        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61        15.95        26.93        35.24        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        19.46         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        14.07        17.75        13.91         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.20        10.92         7.63        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65        32.98        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       10.59         1.51         9.01         8.22        25.02         3.45 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        21.07        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        12.43        17.62        37.05        22.68 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       35.24        17.82         1.64        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49        97.12         1.87        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
        3.22        66.41        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       18.90         2.24        16.27        13.74        92.98        11.31 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN4 
       91.73         6.77        98.99        44.32        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
       13.64         7.36        24.13        27.19        28.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84         2.89        34.06 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        60.16        38.73        35.41         8.52         5.52 

  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                        166.03                         140.81 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                         16.18                          15.65 
[1] "0.4 - 166.0 (16.2)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1"  
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(11Q23.3) MUTATED         0       51        44       47
  DEL PEAK 22(11Q23.3) WILD-TYPE       4       73        83       82
D55V3, multiclass
           clus
vv          DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            51                             73
  STAGE III                           44                             83
  STAGE IV                            47                             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 22(11Q23.3) MUTATED         54  62  22
  DEL PEAK 22(11Q23.3) WILD-TYPE       67 122  31
D55V4, multiclass
          clus
vv         DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  T0+T1+T2                           54                             67
  T3                                 62                            122
  T4                                 22                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 22(11Q23.3) MUTATED    83  16  28   1
  DEL PEAK 22(11Q23.3) WILD-TYPE 141  26  47   7
D55V5, multiclass
    clus
vv   DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  N0                           83                            141
  N1                           16                             26
  N2                           28                             47
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    66   3
  DEL PEAK 22(11Q23.3) WILD-TYPE 119   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     66    3
  DEL PEAK 22(11Q23.3) WILD-TYPE  119    7
   clus
vv  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  0                           66                            119
  1                            3                              7
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    39 106
  DEL PEAK 22(11Q23.3) WILD-TYPE  62 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     39  106
  DEL PEAK 22(11Q23.3) WILD-TYPE   62  182
        clus
vv       DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  FEMALE                           39                             62
  MALE                            106                            182
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q23.3) MUTATED      19                         9   109
  DEL PEAK 22(11Q23.3) WILD-TYPE    23                        12   202
D55V11, multiclass
                           clus
vv                          DEL PEAK 22(11Q23.3) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              109
                           clus
vv                          DEL PEAK 22(11Q23.3) WILD-TYPE
  ASIAN                                                 23
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED     4 127
  DEL PEAK 22(11Q23.3) WILD-TYPE   5 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED      4  127
  DEL PEAK 22(11Q23.3) WILD-TYPE    5  225
                        clus
vv                       DEL PEAK 22(11Q23.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       DEL PEAK 22(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 23(11Q25) MUTATION ANALYSIS
D56V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(11Q25) MUTATED    78  54
  DEL PEAK 23(11Q25) WILD-TYPE 152  99
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         132                          251 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                          54                           99 
$`DEL PEAK 23(11Q25) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       22.29       103.50       105.70        16.83        34.98         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       51.16        33.83         8.35        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C 
       17.56        28.70        24.26         8.98         0.43         0.69 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN 
       12.62        13.12        12.10        11.34        11.34        12.92 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A3IM TCGA-DK-A3IN 
        5.46         2.14        66.41        16.70         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       17.72        50.27        64.18        30.67        15.02       166.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       43.59        15.35         0.49        17.39         0.56         0.66 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       12.99         0.92        13.68        12.95        14.37         8.09 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR 
        8.94         4.01        24.30        22.98        15.58        26.73 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         8.25        18.08        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB 
       13.35         6.15         4.31         6.48        33.01         7.23 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       17.62        21.40        24.92         0.49         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ 
        2.10         7.36        11.31        11.31         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       14.27        21.34        19.82        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV 
       22.72        19.40        38.60         3.06         9.01        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-PQ-A6FI TCGA-SY-A9G5 
        2.76         9.14         9.07        11.70        12.23        31.56 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       86.83        76.01        67.79        65.75       112.83        29.56 
TCGA-UY-A9PE TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 
        4.54        15.35        48.62        12.76        11.90        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
        2.10       110.60        54.90         7.63        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 
        8.32        56.48        61.45        18.81        18.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U 
       30.28        74.56        13.41        20.22        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       63.02        57.90        19.40        47.15        19.17        10.13 

$`DEL PEAK 23(11Q25) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        91.63         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       17.16        27.62        49.12        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        20.48        12.82         9.96        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.46        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       12.26        12.00        11.87        13.08         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        5.19        16.31         1.84        13.58        21.86        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       13.58        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        41.06        38.24        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 
       38.83        24.66         0.10         2.24        16.70        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 
       13.97        14.33         1.22        14.07        15.32        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       16.77        33.04        12.62        22.52        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        27.35        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P 
       53.88        11.01        19.33         5.69        27.45         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86        18.81        12.69        12.36         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       35.24        20.12        66.02         6.94        64.44        19.46 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 
       13.91         3.12        20.98         2.20        10.92         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX 
       27.09        20.05         5.62        10.65        32.98        19.10 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS 
       20.28         8.48        10.59         1.51         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        3.45        27.68         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       11.80        15.32        15.58        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       22.68         3.58        35.24        17.82         1.64        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45       125.49        97.12         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY 
       64.80        79.66         3.22        66.41        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 
       28.24        26.27        18.90         2.24        16.27        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       92.98        10.82        11.31        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       44.32        30.94        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       24.13        27.19        21.86        28.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V 
       52.60        82.49        47.84         2.89        34.06        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        38.73        35.41         8.52         5.52 

  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                        0.43                         0.10 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                      166.03                       140.81 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                       15.35                        15.91 
[1] "0.4 - 166.0 (15.3)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1.1"
D56V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(11Q25) MUTATED         0       47        42       42
  DEL PEAK 23(11Q25) WILD-TYPE       4       77        85       87
D56V3, multiclass
           clus
vv          DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  STAGE I                            0                            4
  STAGE II                          47                           77
  STAGE III                         42                           85
  STAGE IV                          42                           87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  DEL PEAK 23(11Q25) MUTATED         50  58  19
  DEL PEAK 23(11Q25) WILD-TYPE       71 126  34
D56V4, multiclass
          clus
vv         DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  T0+T1+T2                         50                           71
  T3                               58                          126
  T4                               19                           34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 23(11Q25) MUTATED    77  14  24   2
  DEL PEAK 23(11Q25) WILD-TYPE 147  28  51   6
D56V5, multiclass
    clus
vv   DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  N0                         77                          147
  N1                         14                           28
  N2                         24                           51
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    60   3
  DEL PEAK 23(11Q25) WILD-TYPE 125   7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     60    3
  DEL PEAK 23(11Q25) WILD-TYPE  125    7
   clus
vv  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  0                         60                          125
  1                          3                            7
[1] 2 2
[1] FALSE
D56V7, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    37  97
  DEL PEAK 23(11Q25) WILD-TYPE  64 191
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     37   97
  DEL PEAK 23(11Q25) WILD-TYPE   64  191
        clus
vv       DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  FEMALE                         37                           64
  MALE                           97                          191
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q25) MUTATED      20                         9    99
  DEL PEAK 23(11Q25) WILD-TYPE    22                        12   212
D56V11, multiclass
                           clus
vv                          DEL PEAK 23(11Q25) MUTATED
  ASIAN                                             20
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                             99
                           clus
vv                          DEL PEAK 23(11Q25) WILD-TYPE
  ASIAN                                               22
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED     4 119
  DEL PEAK 23(11Q25) WILD-TYPE   5 233
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED      4  119
  DEL PEAK 23(11Q25) WILD-TYPE    5  233
                        clus
vv                       DEL PEAK 23(11Q25) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        119
                        clus
vv                       DEL PEAK 23(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          233
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 24(12P13.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(12P13.1) MUTATED    34  27
  DEL PEAK 24(12P13.1) WILD-TYPE 196 126
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            61                            322 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            27                            126 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA87 TCGA-BT-A20T TCGA-BT-A2LA TCGA-BT-A42C 
       22.29         8.35        47.80        14.89        17.16        28.70 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC 
        0.69        12.62        12.10         5.19         1.84       130.88 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A6AV TCGA-E5-A2PC TCGA-E7-A85H 
       13.58        17.72         9.67        64.18        43.59        12.95 
TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43X 
        8.09        23.41        46.78        19.79        22.98         3.62 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-AA3D TCGA-G2-AA3F 
        5.69        18.08         6.15        12.36        64.44        19.46 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A764 TCGA-GV-A3JW 
       24.92         7.73        20.98         7.36        20.05        21.34 
TCGA-K4-A6FZ TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
        1.81        12.43        22.68        67.79       112.83        17.82 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T3 
       97.12        15.35         1.87        12.76        28.24         2.24 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       10.82       110.60         7.63         8.32         6.77        56.48 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
       11.97        18.64        20.22        19.69         8.61        60.16 
TCGA-ZF-AA52 
       35.41 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        91.63       103.50       105.70        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       24.26        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.43        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        11.34        11.34        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90         7.20         5.46        16.31        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79       123.85        87.32         2.20         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        17.98        29.16         5.52        25.74 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       12.85        27.35        14.96        20.91        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81        12.69         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       14.07        17.75         0.49         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12         2.20        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74        15.42         6.38        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        3.75        31.56        17.62        37.05        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75         3.58        35.24        29.56         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04         6.58        97.45       125.49        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        79.66         3.22        66.41        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        92.98        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.81         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        0.66        13.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        52.60        82.49        47.84         2.89        34.06 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        63.02        38.73        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          0.69                           0.10 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                         17.72                          15.60 
[1] "0.7 - 130.9 (17.7)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(12P13.1) MUTATED         0       15        20       26
  DEL PEAK 24(12P13.1) WILD-TYPE       4      109       107      103
D57V3, multiclass
           clus
vv          DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            15                            109
  STAGE III                           20                            107
  STAGE IV                            26                            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 24(12P13.1) MUTATED         16  30  13
  DEL PEAK 24(12P13.1) WILD-TYPE      105 154  40
D57V4, multiclass
          clus
vv         DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  T0+T1+T2                           16                            105
  T3                                 30                            154
  T4                                 13                             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 24(12P13.1) MUTATED    30   8  16   1
  DEL PEAK 24(12P13.1) WILD-TYPE 194  34  59   7
D57V5, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  N0                           30                            194
  N1                            8                             34
  N2                           16                             59
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    25   2
  DEL PEAK 24(12P13.1) WILD-TYPE 160   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     25    2
  DEL PEAK 24(12P13.1) WILD-TYPE  160    8
   clus
vv  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  0                           25                            160
  1                            2                              8
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    19  43
  DEL PEAK 24(12P13.1) WILD-TYPE  82 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     19   43
  DEL PEAK 24(12P13.1) WILD-TYPE   82  245
        clus
vv       DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  FEMALE                           19                             82
  MALE                             43                            245
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12P13.1) MUTATED       7                         3    51
  DEL PEAK 24(12P13.1) WILD-TYPE    35                        18   260
D57V11, multiclass
                           clus
vv                          DEL PEAK 24(12P13.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               51
                           clus
vv                          DEL PEAK 24(12P13.1) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED     2  58
  DEL PEAK 24(12P13.1) WILD-TYPE   7 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED      2   58
  DEL PEAK 24(12P13.1) WILD-TYPE    7  294
                        clus
vv                       DEL PEAK 24(12P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       DEL PEAK 24(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            294
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 25(12Q24.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(12Q24.33) MUTATED    47  35
  DEL PEAK 25(12Q24.33) WILD-TYPE 183 118
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             82                             301 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             35                             118 
$`DEL PEAK 25(12Q24.33) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A20W TCGA-BT-A2LA 
      103.50        15.12        10.22        47.80         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
       20.48        28.41         1.94         0.43         0.69        12.62 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A2I4 
       12.00        12.10         4.90         7.20         5.19       123.85 
TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-E5-A2PC 
       17.72         9.67        17.98        38.24        15.02        43.59 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3SL 
       15.35        17.39         1.22        13.68         8.09        23.41 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BZ TCGA-FD-A62P 
        5.52        46.78        12.85         3.62        27.45         6.28 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D 
       12.36         2.27         4.31         6.48        17.62        64.44 
TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A76B 
       19.46        15.91        14.07        24.92         0.49         7.36 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-HQ-A5NE 
        5.62         4.73        32.98        21.34        22.72         8.22 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-SY-A9G0 
        9.14         9.07         1.74        15.32        12.23        12.43 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HF TCGA-XF-A8HG 
       22.68        65.75       112.83        17.82        97.12        15.35 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SX TCGA-XF-AAMF TCGA-XF-AAMJ 
       64.80        79.66         3.22        23.64        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 
        7.63         8.32        44.32        56.48        61.45        18.64 
TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       47.84        63.02        35.41        19.17 

$`DEL PEAK 25(12Q24.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 
       49.12         0.62        41.75        51.16        66.54        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
        5.06        14.89        14.96         5.06         8.25        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.46        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.10        12.26        13.12        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       13.08        12.92         5.46        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        50.27        21.30        23.21        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        30.67        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         0.92        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       25.74        19.79        22.98        27.35        14.96        20.91 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         8.25        18.08        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
       13.35        62.86        18.81         6.15        12.69         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        66.02         6.94 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A6I1 
       21.40         2.24        15.81         4.50        17.75         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        38.60         3.06         9.01        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         2.76        27.68        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
        6.38        11.80        15.58        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        31.56        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        76.01        67.79         3.58        35.24        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        4.54         1.64        45.04         6.58        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
        1.87        17.88        48.62        66.41        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64         2.10        13.74        92.98       110.60        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 
       71.57        91.73         2.96         6.77        98.99        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.81         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63         0.66        11.97        13.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
       13.41         3.48        52.73        52.60        82.49        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       38.73        57.90        19.40         8.52        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                           0.43                            0.10 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         123.85                          166.03 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         15.335                          15.950 
[1] "0.4 - 123.8 (15.3)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.1"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(12Q24.33) MUTATED         0       27        16       37
  DEL PEAK 25(12Q24.33) WILD-TYPE       4       97       111       92
D58V3, multiclass
           clus
vv          DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  STAGE I                               0                               4
  STAGE II                             27                              97
  STAGE III                            16                             111
  STAGE IV                             37                              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  DEL PEAK 25(12Q24.33) MUTATED         30  39  11
  DEL PEAK 25(12Q24.33) WILD-TYPE       91 145  42
D58V4, multiclass
          clus
vv         DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  T0+T1+T2                            30                              91
  T3                                  39                             145
  T4                                  11                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 25(12Q24.33) MUTATED    39  12  22   3
  DEL PEAK 25(12Q24.33) WILD-TYPE 185  30  53   5
D58V5, multiclass
    clus
vv   DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  N0                            39                             185
  N1                            12                              30
  N2                            22                              53
  N3                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    35   3
  DEL PEAK 25(12Q24.33) WILD-TYPE 150   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     35    3
  DEL PEAK 25(12Q24.33) WILD-TYPE  150    7
   clus
vv  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  0                            35                             150
  1                             3                               7
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    18  65
  DEL PEAK 25(12Q24.33) WILD-TYPE  83 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     18   65
  DEL PEAK 25(12Q24.33) WILD-TYPE   83  223
        clus
vv       DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  FEMALE                            18                              83
  MALE                              65                             223
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12Q24.33) MUTATED      12                         3    65
  DEL PEAK 25(12Q24.33) WILD-TYPE    30                        18   246
D58V11, multiclass
                           clus
vv                          DEL PEAK 25(12Q24.33) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                65
                           clus
vv                          DEL PEAK 25(12Q24.33) WILD-TYPE
  ASIAN                                                  30
  BLACK OR AFRICAN AMERICAN                              18
  WHITE                                                 246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED     1  76
  DEL PEAK 25(12Q24.33) WILD-TYPE   8 276
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED      1   76
  DEL PEAK 25(12Q24.33) WILD-TYPE    8  276
                        clus
vv                       DEL PEAK 25(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            76
                        clus
vv                       DEL PEAK 25(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             276
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 26(13Q14.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(13Q14.2) MUTATED    87  61
  DEL PEAK 26(13Q14.2) WILD-TYPE 143  92
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           148                            235 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            61                             92 
$`DEL PEAK 26(13Q14.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 
       16.27        16.77        34.98        27.62         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20R 
       15.12        47.80         2.66         6.74        32.84         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06         8.25        17.16         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        28.70        24.26         8.98         1.94 
TCGA-CF-A1HS TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC 
        0.43         5.19         1.84        21.86        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
      112.44        16.14         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 
        2.20         7.82         8.22        17.72         9.67        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6T TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E7-A3X6 
       67.36        30.67        12.36         8.65        43.59        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
        0.49        17.39         0.56        12.99         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.95        14.37        32.02         8.94        33.04         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       22.52        24.30        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       27.35        19.33         5.36         8.25        27.45        58.92 
TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P 
        2.70         6.15        12.36         4.31        17.23         6.48 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       35.24        33.01        19.46        21.40        15.81         4.50 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GV-A3JW 
       24.92         8.94        13.91         2.10         2.20        21.34 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC 
       19.10        10.59        38.60         9.01         8.22         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
       27.68         9.07         1.74         1.81        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M 
       13.48        12.23        16.67         3.75        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        65.75       112.83        35.24        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SW 
        1.64         6.58        97.45        48.62         3.22        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ 
       23.64        21.04         2.24        66.64       110.60        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN7 
        7.63        71.57         6.77        44.32        56.48        18.81 
TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       11.97        28.41         3.48        52.73        52.60        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         2.89        19.69        60.16        63.02        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       57.90        19.40        47.15        19.17 

$`DEL PEAK 26(13Q14.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       44.94        16.83        17.16        49.12        41.75        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 
       10.22        33.83        40.08         7.33        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
       13.15        19.04        12.16        17.88        19.50        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.35        16.18        20.48        28.41        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
       16.31        13.58         2.14        66.41        19.00        16.70 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IT 
       17.62        15.62        10.59        13.58        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
       23.21        20.81        10.55       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       41.56        76.60        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58       166.03        10.49         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       12.03        10.62        15.35        38.83         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
       16.70         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.07        15.32         8.09        16.77        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       60.66        23.41        17.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       11.01         5.69        18.08         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       62.86        18.81        12.69         2.27         3.06         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61        15.95        26.93         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC 
       17.62        66.02         6.94        64.44         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         0.49         7.73         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       14.27        19.82        20.28         8.48        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.07        22.72         1.51        19.40         3.06        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
        3.45        21.24         2.76        11.70        15.42         6.38 
TCGA-K4-AAQO TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       11.80        21.07        14.24         1.84        12.43        31.56 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PE TCGA-XF-A8HB 
       37.05        76.01        67.79         3.58         4.54        45.04 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
      125.49        97.12        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       79.66        66.41        12.76        28.24        26.27        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       16.27         2.10        13.74        92.98        10.82        11.31 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       91.73         2.96         8.32        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL 
       30.28        27.19        21.86        74.56        13.41        82.49 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       34.06         8.61        59.38        35.41         8.52         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        17.195                         15.320 
[1] "0.4 - 130.9 (17.2)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(13Q14.2) MUTATED         0       41        49       56
  DEL PEAK 26(13Q14.2) WILD-TYPE       4       83        78       73
D59V3, multiclass
           clus
vv          DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            41                             83
  STAGE III                           49                             78
  STAGE IV                            56                             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 26(13Q14.2) MUTATED         43  80  16
  DEL PEAK 26(13Q14.2) WILD-TYPE       78 104  37
D59V4, multiclass
          clus
vv         DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  T0+T1+T2                           43                             78
  T3                                 80                            104
  T4                                 16                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 26(13Q14.2) MUTATED    73  18  35   4
  DEL PEAK 26(13Q14.2) WILD-TYPE 151  24  40   4
D59V5, multiclass
    clus
vv   DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  N0                           73                            151
  N1                           18                             24
  N2                           35                             40
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED    64   2
  DEL PEAK 26(13Q14.2) WILD-TYPE 121   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED     64    2
  DEL PEAK 26(13Q14.2) WILD-TYPE  121    8
   clus
vv  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  0                           64                            121
  1                            2                              8
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED    37 111
  DEL PEAK 26(13Q14.2) WILD-TYPE  64 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED     37  111
  DEL PEAK 26(13Q14.2) WILD-TYPE   64  177
        clus
vv       DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  FEMALE                           37                             64
  MALE                            111                            177
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(13Q14.2) MUTATED      11                        13   116
  DEL PEAK 26(13Q14.2) WILD-TYPE    31                         8   195
D59V11, multiclass
                           clus
vv                          DEL PEAK 26(13Q14.2) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              116
                           clus
vv                          DEL PEAK 26(13Q14.2) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED     5 127
  DEL PEAK 26(13Q14.2) WILD-TYPE   4 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED      5  127
  DEL PEAK 26(13Q14.2) WILD-TYPE    4  225
                        clus
vv                       DEL PEAK 26(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       DEL PEAK 26(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 27(14Q24.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(14Q24.1) MUTATED    75  51
  DEL PEAK 27(14Q24.1) WILD-TYPE 155 102
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           126                            257 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            51                            102 
$`DEL PEAK 27(14Q24.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.77         0.62        41.75        51.16        15.12        47.80 
TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK 
       19.04        14.89         5.06         8.35        16.18         9.96 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HY TCGA-CU-A0YO 
        0.46         0.43        12.62        13.12        11.34         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        7.20         5.19         1.84        21.86         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 
      130.88       112.44        10.59        17.72        50.27        48.00 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4TZ 
       64.18        41.06       166.03        10.49        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A85H TCGA-E7-A8O7 
       38.83         0.49        12.99         0.92        12.95        15.32 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       24.30        29.16        25.74        46.78        19.79        22.98 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       20.91        15.58        18.08        58.92         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.15         3.06         4.31        31.07        17.23         6.48 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3RD 
       61.94        20.12        17.62        66.02        64.44        14.07 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-AATP TCGA-GV-A3JZ 
        0.49         7.73         7.36        11.31        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       20.28        10.59         8.58        19.07        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI 
       38.60         3.06         3.45        15.42        13.48        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HF 
       22.68        86.83        17.82         4.54         1.64        97.12 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ 
        1.87        48.62        23.64        28.24        26.27        54.90 
TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        7.63         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       61.45        86.30        13.64         7.36        28.41        74.56 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84        20.22         2.89        19.69        38.73        35.41 

$`DEL PEAK 27(14Q24.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       91.63        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       49.12        66.54        10.22        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        2.66         6.74        12.39         6.58        13.15        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
       17.16        20.48         4.67        12.82        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       24.26        28.41         8.98         1.94        23.01         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA 
       10.95        12.66        12.46        12.10        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ 
       12.10        11.34        11.87        13.08        12.92         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       16.31        13.58        66.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         7.82         8.22        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       13.58        12.36         8.65         7.53        13.64        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       10.62        43.59        24.66         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       17.39         0.56         0.66        14.56        13.97        14.33 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
        1.22        13.68        14.07        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SS 
       27.98        60.66        23.41        17.98         5.52        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       19.33         5.36         5.69         8.25        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        7.10        13.35        18.81        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        9.67        10.85         7.13        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.91        17.75        24.92         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        10.92        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        27.35         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22        25.02        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       27.68         9.07        11.70         1.74         1.81         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 
       11.80        15.32        15.58        21.07        16.67         3.75 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        67.79        65.75         3.58       112.83        35.24 
TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       29.56        45.04         6.58        97.45       125.49        15.35 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       17.88        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        21.04        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       71.57        91.73         2.96        30.94        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.81         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.41         3.48        52.73        52.60        82.49        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 
        8.61        59.38        60.16        63.02        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                        166.03                         140.81 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                         17.67                          14.96 
[1] "0.4 - 166.0 (17.7)" "0.1 - 140.8 (15.0)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 27(14Q24.1) MUTATED         1       36        38       49
  DEL PEAK 27(14Q24.1) WILD-TYPE       3       88        89       80
D60V3, multiclass
           clus
vv          DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            36                             88
  STAGE III                           38                             89
  STAGE IV                            49                             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 27(14Q24.1) MUTATED         40  59  17
  DEL PEAK 27(14Q24.1) WILD-TYPE       81 125  36
D60V4, multiclass
          clus
vv         DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  T0+T1+T2                           40                             81
  T3                                 59                            125
  T4                                 17                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 27(14Q24.1) MUTATED    67   9  38   1
  DEL PEAK 27(14Q24.1) WILD-TYPE 157  33  37   7
D60V5, multiclass
    clus
vv   DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  N0                           67                            157
  N1                            9                             33
  N2                           38                             37
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED    61   2
  DEL PEAK 27(14Q24.1) WILD-TYPE 124   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED     61    2
  DEL PEAK 27(14Q24.1) WILD-TYPE  124    8
   clus
vv  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  0                           61                            124
  1                            2                              8
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED    26 101
  DEL PEAK 27(14Q24.1) WILD-TYPE  75 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED     26  101
  DEL PEAK 27(14Q24.1) WILD-TYPE   75  187
        clus
vv       DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  FEMALE                           26                             75
  MALE                            101                            187
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(14Q24.1) MUTATED      14                         5   102
  DEL PEAK 27(14Q24.1) WILD-TYPE    28                        16   209
D60V11, multiclass
                           clus
vv                          DEL PEAK 27(14Q24.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                              102
                           clus
vv                          DEL PEAK 27(14Q24.1) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED     3 112
  DEL PEAK 27(14Q24.1) WILD-TYPE   6 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED      3  112
  DEL PEAK 27(14Q24.1) WILD-TYPE    6  240
                        clus
vv                       DEL PEAK 27(14Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 27(14Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            240
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 28(15Q13.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(15Q13.1) MUTATED    94  54
  DEL PEAK 28(15Q13.1) WILD-TYPE 136  99
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           148                            235 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                            54                             99 
$`DEL PEAK 28(15Q13.1) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A0C8 
        8.35        27.62        51.16        15.12        47.80        40.08 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A20X 
        2.66         6.58        19.04        32.84         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
       16.18        20.48        17.56        28.70        24.26         8.98 
TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.94        12.62         7.20         5.19        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN 
      112.44         1.81         7.79       123.85         7.82         8.22 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6W 
       17.98        15.68        41.06        30.67        15.02         8.65 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       43.50        12.03        43.59         0.49        17.39         0.56 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 
       12.99         1.22        13.68        12.95         8.09        32.02 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N 
       22.52        60.66        24.30        29.16        25.74        22.98 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        7.10        13.35        12.69         4.31        10.85        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY 
       17.23         6.48        61.94        26.93        20.12        17.62 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       66.02        15.81         4.50        14.07        24.92         8.94 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 
        2.10         2.20         7.36        10.92         7.63         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        10.65        21.34        19.10        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
        8.58        19.07        22.72        19.40        38.60         8.22 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       25.02         2.76         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       15.42        15.32        15.58        13.48        16.67        14.24 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HD 
       35.24        29.56        17.82         4.54        45.04        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SX 
       97.12        15.35         1.87        48.62         3.22        23.64 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       26.27         2.24        66.64        54.90         7.63         2.96 
TCGA-XF-AAN2 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF 
       61.45        11.97        13.64        28.41        74.56        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       52.60        82.49         2.89        34.06        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        35.41        47.15        19.17 

$`DEL PEAK 28(15Q13.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I 
        0.62        41.75        66.54        10.22        33.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        12.39        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH 
        5.06        14.89        14.96         5.06        17.16         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82         9.96        28.41        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       13.08        12.92         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58        21.86         2.14        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK 
       16.14        17.62        15.62        10.59        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       76.60        67.36        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       10.49         7.53        13.64        10.62        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         2.24        16.70         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       13.97        14.33         0.92        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       16.77         8.94        33.04         4.01        12.62        27.98 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98         5.52        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA 
       53.88        11.01        19.33         5.69         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81         6.15        12.36         2.27         3.06         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13        10.65         8.94         3.25        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       35.24        33.01         7.23         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 
       21.40         2.24        15.91        17.75         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        7.73         3.12        20.98        11.31        11.31        27.09 
TCGA-GU-A764 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI 
       20.05        32.98         7.00        14.27        19.82        10.59 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35         1.51         3.06         9.01         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FI 
        9.14        27.68         6.38        11.80        21.07        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
        1.84         3.75        31.56        67.79        65.75         3.58 
TCGA-UY-A8OD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH 
      112.83         1.64         6.58       125.49        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
       79.66        66.41        12.76        11.90        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
      110.60        11.31        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U 
       21.86        13.41         3.48        47.84        20.22         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        38.73        57.90        19.40         8.52         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                        123.85                         166.03 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                         17.31                          14.96 
[1] "0.5 - 123.8 (17.3)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.2"
D61V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 28(15Q13.1) MUTATED         1       43        49       55
  DEL PEAK 28(15Q13.1) WILD-TYPE       3       81        78       74
D61V3, multiclass
           clus
vv          DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            43                             81
  STAGE III                           49                             78
  STAGE IV                            55                             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 28(15Q13.1) MUTATED         41  75  16
  DEL PEAK 28(15Q13.1) WILD-TYPE       80 109  37
D61V4, multiclass
          clus
vv         DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  T0+T1+T2                           41                             80
  T3                                 75                            109
  T4                                 16                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 28(15Q13.1) MUTATED    76  17  34   4
  DEL PEAK 28(15Q13.1) WILD-TYPE 148  25  41   4
D61V5, multiclass
    clus
vv   DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  N0                           76                            148
  N1                           17                             25
  N2                           34                             41
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED    54   3
  DEL PEAK 28(15Q13.1) WILD-TYPE 131   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED     54    3
  DEL PEAK 28(15Q13.1) WILD-TYPE  131    7
   clus
vv  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  0                           54                            131
  1                            3                              7
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED    39 110
  DEL PEAK 28(15Q13.1) WILD-TYPE  62 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED     39  110
  DEL PEAK 28(15Q13.1) WILD-TYPE   62  178
        clus
vv       DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  FEMALE                           39                             62
  MALE                            110                            178
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(15Q13.1) MUTATED      10                         5   125
  DEL PEAK 28(15Q13.1) WILD-TYPE    32                        16   186
D61V11, multiclass
                           clus
vv                          DEL PEAK 28(15Q13.1) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                              125
                           clus
vv                          DEL PEAK 28(15Q13.1) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED     5 133
  DEL PEAK 28(15Q13.1) WILD-TYPE   4 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED      5  133
  DEL PEAK 28(15Q13.1) WILD-TYPE    4  219
                        clus
vv                       DEL PEAK 28(15Q13.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 28(15Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            219
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 29(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16P13.3) MUTATED    96  67
  DEL PEAK 29(16P13.3) WILD-TYPE 134  86
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           163                            220 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                            67                             86 
$`DEL PEAK 29(16P13.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W 
       22.29        11.97         8.35        16.27        16.77        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J 
       41.75        15.12        10.22        47.80        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
        6.58        32.84         5.06         8.35        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HS 
        4.67        12.82        28.70        24.26        23.01         0.43 
TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       12.66        11.34        11.87        12.92         5.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 
        1.84        21.86        18.41         1.81       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WX 
        2.20         7.82         8.22        21.30         9.67        10.55 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       17.98        67.36        30.67        15.02        13.58       166.03 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       12.03        15.35        38.83        17.39         0.56        12.99 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U 
       32.02        33.04        25.74        19.79        22.98        20.91 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       15.58        26.73         5.36         8.25        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        7.10        13.35        12.69        12.36         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3RB 
       10.85        31.07        61.94        26.93        20.12         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        24.92         0.49         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
        2.10         2.20        10.92        11.31         7.63         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        32.98        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
        8.48        22.72        19.40        38.60         3.06        25.02 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX 
       11.80        15.32        15.58        13.48        16.67         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD 
       12.43        31.56        22.68        86.83        65.75       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       35.24        29.56        17.82         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       97.12        15.35        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMT 
       28.24        26.27         2.24         2.10         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32         6.77        44.32        56.48        61.45        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RF 
       18.81        11.97        13.64        21.11        74.56        52.73 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       82.49        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        63.02        38.73        57.90        19.40        47.15 
TCGA-ZF-AA5H 
       19.17 

$`DEL PEAK 29(16P13.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       91.63       103.50       105.70        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 
       34.98        49.12         0.62        51.16        66.54        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74        12.39        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50        14.89        14.96         5.06         8.25 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       20.48         9.96        17.56        28.41         8.98         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.46         0.69        10.95        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.34        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90         7.20        16.31        13.58         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62        10.59         7.79        13.58        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21        20.81       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA6U 
       76.60        15.68        41.06        38.24        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65         7.53        13.64        43.50        10.62        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       24.66         0.10         0.49         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ 
       24.30        23.41        17.98        29.16         5.52        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35        14.96         3.62        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       19.33         5.69        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       18.81         6.15         3.06         9.67         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25         6.48        30.61        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC 
       64.44        19.46        21.40         2.24        15.81        17.75 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 
       13.91         3.12        20.98         7.36        11.31        27.09 
TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       20.05         7.00        14.27        20.28        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
        8.58        19.07         1.51         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI 
       21.24         2.76        15.42         6.38        21.07        12.23 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       14.24         3.75        17.62        37.05        76.01        67.79 
TCGA-UY-A8OC TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.58        45.04        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9T2 
       48.62        64.80         3.22        66.41        12.76        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 
       11.31        54.90        71.57        91.73        98.99        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4W 
       28.41        13.41         3.48        52.60        34.06        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41         8.52         5.52        10.13 

  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                        166.03                         140.81 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                        15.580                         15.745 
[1] "0.4 - 166.0 (15.6)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1.1"
D62V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 29(16P13.3) MUTATED         1       45        57       58
  DEL PEAK 29(16P13.3) WILD-TYPE       3       79        70       71
D62V3, multiclass
           clus
vv          DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            45                             79
  STAGE III                           57                             70
  STAGE IV                            58                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 29(16P13.3) MUTATED         42 86 22
  DEL PEAK 29(16P13.3) WILD-TYPE       79 98 31
D62V4, multiclass
          clus
vv         DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  T0+T1+T2                           42                             79
  T3                                 86                             98
  T4                                 22                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 29(16P13.3) MUTATED    85  13  43   2
  DEL PEAK 29(16P13.3) WILD-TYPE 139  29  32   6
D62V5, multiclass
    clus
vv   DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  N0                           85                            139
  N1                           13                             29
  N2                           43                             32
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED    66   3
  DEL PEAK 29(16P13.3) WILD-TYPE 119   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED     66    3
  DEL PEAK 29(16P13.3) WILD-TYPE  119    7
   clus
vv  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  0                           66                            119
  1                            3                              7
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED    45 118
  DEL PEAK 29(16P13.3) WILD-TYPE  56 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED     45  118
  DEL PEAK 29(16P13.3) WILD-TYPE   56  170
        clus
vv       DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  FEMALE                           45                             56
  MALE                            118                            170
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16P13.3) MUTATED      10                         6   140
  DEL PEAK 29(16P13.3) WILD-TYPE    32                        15   171
D62V11, multiclass
                           clus
vv                          DEL PEAK 29(16P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              140
                           clus
vv                          DEL PEAK 29(16P13.3) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED     3 149
  DEL PEAK 29(16P13.3) WILD-TYPE   6 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED      3  149
  DEL PEAK 29(16P13.3) WILD-TYPE    6  203
                        clus
vv                       DEL PEAK 29(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 29(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 30(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q23.1) MUTATED    66  46
  DEL PEAK 30(16Q23.1) WILD-TYPE 164 107
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           112                            271 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            46                            107 
$`DEL PEAK 30(16Q23.1) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       16.27        16.77         0.62        41.75        15.12        10.22 
TCGA-BL-A0C8 TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC 
       40.08        12.92         5.19         1.84        21.86       130.88 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
        1.81        10.59         7.79       123.85        87.32         8.22 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P 
        9.67        20.81        17.98        67.36        30.67        15.02 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       10.49         8.65        12.03        15.35         0.49        17.39 
TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3N5 
       14.56        12.99        13.68        12.95         8.94        22.52 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62O 
        5.52        12.85        22.98        20.91         2.70         7.10 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF 
        6.15        12.69        12.36        31.07         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 
       30.61        20.12        15.91        14.07         2.10         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       10.92        11.31         7.63         5.62         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ 
       19.10        19.82        20.28         8.48        10.59        19.40 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       38.60        21.24         9.14        11.70         1.74         1.81 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB 
       15.58        13.48        12.23        12.43        86.83        65.75 
TCGA-UY-A9PA TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       35.24         1.64         6.58       125.49        97.12        15.35 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       79.66         3.22        11.90        23.64        21.04        26.27 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN3 
        2.10        10.82       110.60         7.63        56.48        86.30 
TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.81         0.66        11.97        13.64        30.28        74.56 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
        3.48        52.73         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
       60.16        63.02        38.73        57.90 

$`DEL PEAK 30(16Q23.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J 
       51.16        66.54        47.80        33.83         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       11.87        13.08         4.90         7.20         5.46        16.31 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44        16.14        17.62        15.62         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WX 
        7.82        17.72        50.27        21.30        23.21        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        48.00        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X 
       41.06        38.24        13.58       166.03        12.36         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        0.10         2.24        16.70         0.56         0.66        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         0.92         1.22        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       25.74        46.78        19.79        27.35        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        5.69         8.25        27.45        18.08        58.92         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       13.35        62.86        18.81         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
        2.24        15.81         4.50        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
        8.94        13.91         7.73         3.12        20.98         7.36 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       11.31        27.09        20.05         4.73        10.65        32.98 
TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       21.34        27.35         8.58        19.07        22.72         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22        25.02         3.45         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
       27.68         9.07        15.42         6.38        11.80        15.32 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        16.67        14.24         1.84         3.75        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       17.62        37.05        22.68        76.01        67.79         3.58 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HD 
      112.83        29.56        17.82         4.54        45.04        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV 
        1.87        17.88        48.62        64.80        66.41        12.76 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 
       28.24        18.90         2.24        16.27        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R0 
       27.06        75.39         3.88        18.84         9.63        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       13.41        52.60        82.49        47.84        20.22        34.06 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                         14.17                          16.67 
[1] "0.5 - 130.9 (14.2)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 30(16Q23.1) MUTATED         2       36        34       39
  DEL PEAK 30(16Q23.1) WILD-TYPE       2       88        93       90
D63V3, multiclass
           clus
vv          DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  STAGE I                              2                              2
  STAGE II                            36                             88
  STAGE III                           34                             93
  STAGE IV                            39                             90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 30(16Q23.1) MUTATED         31  51  16
  DEL PEAK 30(16Q23.1) WILD-TYPE       90 133  37
D63V4, multiclass
          clus
vv         DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  T0+T1+T2                           31                             90
  T3                                 51                            133
  T4                                 16                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 30(16Q23.1) MUTATED    53  11  24   3
  DEL PEAK 30(16Q23.1) WILD-TYPE 171  31  51   5
D63V5, multiclass
    clus
vv   DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  N0                           53                            171
  N1                           11                             31
  N2                           24                             51
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    46   3
  DEL PEAK 30(16Q23.1) WILD-TYPE 139   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     46    3
  DEL PEAK 30(16Q23.1) WILD-TYPE  139    7
   clus
vv  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  0                           46                            139
  1                            3                              7
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    20  92
  DEL PEAK 30(16Q23.1) WILD-TYPE  81 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     20   92
  DEL PEAK 30(16Q23.1) WILD-TYPE   81  196
        clus
vv       DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  FEMALE                           20                             81
  MALE                             92                            196
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q23.1) MUTATED       8                         4    97
  DEL PEAK 30(16Q23.1) WILD-TYPE    34                        17   214
D63V11, multiclass
                           clus
vv                          DEL PEAK 30(16Q23.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               97
                           clus
vv                          DEL PEAK 30(16Q23.1) WILD-TYPE
  ASIAN                                                 34
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED     5  99
  DEL PEAK 30(16Q23.1) WILD-TYPE   4 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED      5   99
  DEL PEAK 30(16Q23.1) WILD-TYPE    4  253
                        clus
vv                       DEL PEAK 30(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 30(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 31(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(17P12) MUTATED   118  76
  DEL PEAK 31(17P12) WILD-TYPE 112  77
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         194                          189 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                          76                           77 
$`DEL PEAK 31(17P12) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7S 
       22.29       103.50       105.70        16.27        17.16        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J 
        0.62        51.16        15.12        47.80        40.08         2.66 
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       12.39        19.04        32.84        17.88        19.50        14.89 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        17.16        16.18         4.67         9.96        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
        8.98         1.94         0.46         0.43         0.69        12.62 
TCGA-CF-A5UA TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.00         5.46         1.84         2.14        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
       16.70       130.88       112.44         1.81        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20        13.58         8.22        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 
        9.67        48.00        17.98        64.18        41.06        30.67 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58       166.03        10.49         7.53        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       43.59        15.35        38.83         0.49        17.39         0.56 
TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
       14.56        12.99         0.92        13.68        12.95         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
       16.77         8.94        60.66        24.30        29.16         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       46.78        12.85        22.98        27.35        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       26.73         5.36         8.25         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK 
       62.86        18.81         6.15        12.69         3.06        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       31.07        10.65        61.94        30.61        26.93        35.24 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       20.12        17.62        66.02        64.44        21.40         4.50 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        24.92         0.49        13.91         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        32.98         7.00        19.82        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        19.07        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
        8.22         9.14        11.70         1.74        15.42        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        12.43        31.56 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        76.01        67.79        65.75         3.58       112.83 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       17.82         4.54         1.64        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SX 
       15.35         1.87        48.62        79.66         3.22        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ 
       28.24         2.24        10.82       110.60        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       30.94        86.30        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       24.13        21.86        28.41         3.48        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA51 
       47.84        20.22         2.89        19.69        60.16        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA56 
       57.90         8.52 

$`DEL PEAK 31(17P12) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       11.97        91.63         8.35        44.94        16.83        16.77 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 
       27.62        49.12        41.75        66.54        10.22        33.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R 
        7.33         6.74         6.58        13.15        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         5.06         8.35        20.48        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       28.70        28.41        23.01        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.10        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       11.87        13.08        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF 
       16.31        13.58        21.86        19.00        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW 
       15.62         7.79       123.85         7.82        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       140.81        41.56        76.60        67.36        15.68 
TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       38.24        12.36         8.65        13.64        43.50        10.62 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       24.66         0.10         2.24        16.70         0.66        13.97 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       14.33         1.22        14.07        15.32        14.37        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
       33.04         4.01        12.62        22.52        27.98        23.41 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
       17.98        25.74        19.79        14.96        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01        19.33         5.69        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        2.70        12.36         2.27         4.31         9.67         7.13 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES 
       17.23         8.94         3.25         6.48        15.95        33.01 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23         6.94        19.46         2.24        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A763 TCGA-GU-A764 
       17.75         8.94         3.12        20.98        27.09        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        5.62        10.65        14.27        21.34        19.10        10.59 
TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35        22.72         1.51        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        2.76        27.68         9.07         1.81         6.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       15.58        21.07        13.48         3.75        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       86.83        35.24        29.56        45.04         6.58        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        66.41        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       11.31         7.63         6.77        61.45        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R2 
       18.81         3.88        18.84         9.63         0.66        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-AA4R 
       30.28        27.19        74.56        13.41        52.73        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
        8.61        59.38        63.02        35.41        19.40        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                        0.43                         0.10 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                      166.03                       140.81 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                      16.225                       15.620 
[1] "0.4 - 166.0 (16.2)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D64V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 31(17P12) MUTATED         2       59        60       71
  DEL PEAK 31(17P12) WILD-TYPE       2       65        67       58
D64V3, multiclass
           clus
vv          DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  STAGE I                            2                            2
  STAGE II                          59                           65
  STAGE III                         60                           67
  STAGE IV                          71                           58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  DEL PEAK 31(17P12) MUTATED         55 91 31
  DEL PEAK 31(17P12) WILD-TYPE       66 93 22
D64V4, multiclass
          clus
vv         DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  T0+T1+T2                         55                           66
  T3                               91                           93
  T4                               31                           22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 31(17P12) MUTATED   106  19  46   4
  DEL PEAK 31(17P12) WILD-TYPE 118  23  29   4
D64V5, multiclass
    clus
vv   DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  N0                        106                          118
  N1                         19                           23
  N2                         46                           29
  N3                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                              cls
clus                            0  1
  DEL PEAK 31(17P12) MUTATED   92  4
  DEL PEAK 31(17P12) WILD-TYPE 93  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     92    4
  DEL PEAK 31(17P12) WILD-TYPE   93    6
   clus
vv  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  0                         92                           93
  1                          4                            6
[1] 2 2
[1] FALSE
D64V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED    56 140
  DEL PEAK 31(17P12) WILD-TYPE  45 148
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     56  140
  DEL PEAK 31(17P12) WILD-TYPE   45  148
        clus
vv       DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  FEMALE                         56                           45
  MALE                          140                          148
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17P12) MUTATED      18                        11   154
  DEL PEAK 31(17P12) WILD-TYPE    24                        10   157
D64V11, multiclass
                           clus
vv                          DEL PEAK 31(17P12) MUTATED
  ASIAN                                             18
  BLACK OR AFRICAN AMERICAN                         11
  WHITE                                            154
                           clus
vv                          DEL PEAK 31(17P12) WILD-TYPE
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED     6 172
  DEL PEAK 31(17P12) WILD-TYPE   3 180
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED      6  172
  DEL PEAK 31(17P12) WILD-TYPE    3  180
                        clus
vv                       DEL PEAK 31(17P12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        172
                        clus
vv                       DEL PEAK 31(17P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          180
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 32(18Q23) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(18Q23) MUTATED   107  59
  DEL PEAK 32(18Q23) WILD-TYPE 123  94
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         166                          217 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          59                           94 
$`DEL PEAK 32(18Q23) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R 
       22.29        91.63       103.50         8.35        16.27        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 
       34.98        27.62        51.16        66.54        10.22        40.08 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20W 
        2.66        13.15        19.04        32.84         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       17.16        17.56        28.70        24.26         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN 
       10.95        12.66        11.34        11.34        11.87        12.92 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
        7.20         1.84        13.58         2.14        18.41        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62         1.81        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20        13.58         7.82         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       21.30        48.00        64.18        15.68        41.06        15.02 
TCGA-DK-AA6S TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A541 
      166.03         7.53        43.50        43.59        24.66        17.39 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 
        0.56        14.56         1.22        12.95         8.09        16.77 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
        4.01        60.66        24.30        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A62N TCGA-FD-A62O 
       46.78        12.85        22.98        15.58         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF 
       13.35        62.86        12.69         3.06         4.31        17.23 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RC 
       61.94        20.12        66.02        19.46        21.40        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       14.07        24.92         0.49         8.94        13.91         2.10 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
       20.98         2.20        10.92         7.63        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        32.98        21.34        19.10        19.82 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.07        22.72        19.40        38.60         3.06        25.02 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V 
        9.07        11.70         1.74        11.80        15.32        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O 
       12.23        16.67        14.24        12.43        31.56        76.01 
TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       65.75        29.56        17.82         4.54         1.64         6.58 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T5 TCGA-XF-A9T6 
       97.12         3.22        11.90        23.64        66.64         2.10 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        6.77        44.32        86.30        11.97        13.64        18.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RL 
       21.11        21.86        28.41        13.41        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84         2.89         8.61        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       57.90        19.40        47.15        19.17 

$`DEL PEAK 32(18Q23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7Y 
       11.97       105.70        44.94        16.83        16.77        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I 
        0.62        41.75        15.12        47.80        33.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        12.39         6.58        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89        14.96         5.06         8.25        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        12.82         9.96        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       23.01         0.69        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ 
       13.12        12.00        12.10        13.08         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AG 
        5.19        16.31        21.86        66.41        19.00        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        7.79       123.85        17.72        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        17.98        41.56        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       30.67        38.24        13.58        12.36        10.49         8.65 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       13.64        12.03        10.62        15.35        38.83         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME 
        0.49         2.24        16.70         0.66        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       14.33         0.92        13.68        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02         8.94        33.04        12.62        22.52        27.98 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       23.41        17.98        19.79        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        5.69         8.25        27.45        18.08        58.92         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         6.15        12.36         2.27         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.62         6.94        64.44         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
       17.75         7.73         3.12         7.36        11.31        11.31 
TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       27.09         7.00        14.27        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       27.35         8.58         1.51         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         2.76         9.14        27.68         1.81        15.42 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K 
        6.38        15.58        21.07         1.84         3.75        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        86.83        67.79         3.58       112.83 
TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       35.24        45.04        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV 
       17.88        48.62        64.80        79.66        66.41        12.76 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMW TCGA-XF-AAMY 
       13.74        92.98        10.82        11.31         8.32        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        3.88        18.84         9.63         0.66         7.36        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN 
       30.28        27.19        74.56         3.48        52.73        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5N 
       34.06        19.69        59.38        63.02         8.52         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                        0.43                         0.10 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      166.03                       140.81 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      16.965                       15.120 
[1] "0.4 - 166.0 (17.0)" "0.1 - 140.8 (15.1)"
[1] "hr=" "1.3"
D65V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 32(18Q23) MUTATED         1       50        57       58
  DEL PEAK 32(18Q23) WILD-TYPE       3       74        70       71
D65V3, multiclass
           clus
vv          DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  STAGE I                            1                            3
  STAGE II                          50                           74
  STAGE III                         57                           70
  STAGE IV                          58                           71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  DEL PEAK 32(18Q23) MUTATED         50 87 21
  DEL PEAK 32(18Q23) WILD-TYPE       71 97 32
D65V4, multiclass
          clus
vv         DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  T0+T1+T2                         50                           71
  T3                               87                           97
  T4                               21                           32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 32(18Q23) MUTATED    96  16  37   4
  DEL PEAK 32(18Q23) WILD-TYPE 128  26  38   4
D65V5, multiclass
    clus
vv   DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  N0                         96                          128
  N1                         16                           26
  N2                         37                           38
  N3                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    82   1
  DEL PEAK 32(18Q23) WILD-TYPE 103   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     82    1
  DEL PEAK 32(18Q23) WILD-TYPE  103    9
   clus
vv  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  0                         82                          103
  1                          1                            9
[1] 2 2
[1] FALSE
D65V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    46 123
  DEL PEAK 32(18Q23) WILD-TYPE  55 165
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     46  123
  DEL PEAK 32(18Q23) WILD-TYPE   55  165
        clus
vv       DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  FEMALE                         46                           55
  MALE                          123                          165
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(18Q23) MUTATED      17                        10   136
  DEL PEAK 32(18Q23) WILD-TYPE    25                        11   175
D65V11, multiclass
                           clus
vv                          DEL PEAK 32(18Q23) MUTATED
  ASIAN                                             17
  BLACK OR AFRICAN AMERICAN                         10
  WHITE                                            136
                           clus
vv                          DEL PEAK 32(18Q23) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED     5 151
  DEL PEAK 32(18Q23) WILD-TYPE   4 201
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED      5  151
  DEL PEAK 32(18Q23) WILD-TYPE    4  201
                        clus
vv                       DEL PEAK 32(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        151
                        clus
vv                       DEL PEAK 32(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          201
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 33(19P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(19P13.3) MUTATED    74  64
  DEL PEAK 33(19P13.3) WILD-TYPE 156  89
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           138                            245 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            64                             89 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-BL-A0C8 
        8.35        27.62         0.62        51.16        47.80        40.08 
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.39        19.04         5.06        14.89         5.06         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       16.18        20.48         4.67         9.96        17.56        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-DK-A1A5 
       28.41         8.98        23.01         0.46         0.43         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IQ 
       18.41        16.70       112.44        87.32        13.58        17.72 
TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       21.30        48.00        17.98        41.06        38.24        13.58 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ 
        8.65         7.53        12.03        43.59        15.35         0.49 
TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B6 
        1.22        12.95        14.37         8.09        16.77        33.04 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS 
       24.30        23.41        17.98        29.16         5.52        12.85 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       22.98        15.58         5.36         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       58.92        18.81         6.15        12.36         2.27         4.31 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2ES 
       10.65        17.23         8.94         6.48        61.94        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB 
        7.23        20.12        17.62        19.46         2.24         4.50 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       24.92         8.94        10.92        11.31        11.31         7.63 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G 
       10.65         7.00        21.34        19.10        19.82        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A54R TCGA-K4-A5RH 
        1.51        19.40         9.01        25.02        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        1.74        15.42        13.48        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
        3.75        31.56        37.05        22.68        86.83        67.79 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       65.75       112.83        35.24        29.56         1.64        45.04 
TCGA-XF-A8HF TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW 
       97.12        48.62        64.80         3.22        12.76        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMX 
       66.64         2.10       110.60        54.90         2.96         6.77 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RL 
       86.30        13.64        30.28        28.41        74.56        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA53 TCGA-ZF-AA5H 
       47.84        34.06        19.69        59.38        57.90        19.17 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        49.12 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I 
       41.75        66.54        15.12        10.22        33.83         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ 
       17.88        19.50        14.96         8.25        17.16        12.82 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       28.70         1.94         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        19.00       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        7.82         8.22        50.27        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        30.67        15.02       166.03        12.36        10.49 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        43.50        10.62        38.83        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99        14.33         0.92        13.68        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.32        32.02         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       27.98        60.66        25.74        46.78        19.79        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        12.69         3.06         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        7.13         3.25        30.61        15.95        26.93        35.24 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        64.44        21.40        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         0.49        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A763 TCGA-GU-A764 
        3.12        20.98         2.20         7.36        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QH 
        5.62         4.73        32.98        14.27        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF 
       10.59        27.35         8.58        22.72        38.60         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RI 
        8.22         3.45        21.24         2.76         9.14        11.70 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         6.38        11.80        15.32        15.58        21.07 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A9PD 
        1.84        12.43        17.62        76.01         3.58        17.82 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
        4.54         6.58        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        79.66        66.41        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
       10.82        11.31         7.63        71.57        91.73         8.32 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       98.99        44.32        56.48        30.94        61.45        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       11.97        18.64         7.36        21.11        24.13        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
       21.86        13.41         3.48        52.73        52.60        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        60.16        63.02        38.73        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15         5.52        10.13 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        112.83                         166.03 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                         17.59                          15.12 
[1] "0.4 - 112.8 (17.6)" "0.1 - 166.0 (15.1)"
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 33(19P13.3) MUTATED         1       34        43       58
  DEL PEAK 33(19P13.3) WILD-TYPE       3       90        84       71
D66V3, multiclass
           clus
vv          DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  STAGE I                              1                              3
  STAGE II                            34                             90
  STAGE III                           43                             84
  STAGE IV                            58                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 33(19P13.3) MUTATED         33  72  23
  DEL PEAK 33(19P13.3) WILD-TYPE       88 112  30
D66V4, multiclass
          clus
vv         DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  T0+T1+T2                           33                             88
  T3                                 72                            112
  T4                                 23                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 33(19P13.3) MUTATED    68  23  30   5
  DEL PEAK 33(19P13.3) WILD-TYPE 156  19  45   3
D66V5, multiclass
    clus
vv   DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  N0                           68                            156
  N1                           23                             19
  N2                           30                             45
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    53   7
  DEL PEAK 33(19P13.3) WILD-TYPE 132   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     53    7
  DEL PEAK 33(19P13.3) WILD-TYPE  132    3
   clus
vv  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  0                           53                            132
  1                            7                              3
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    37 102
  DEL PEAK 33(19P13.3) WILD-TYPE  64 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     37  102
  DEL PEAK 33(19P13.3) WILD-TYPE   64  186
        clus
vv       DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  FEMALE                           37                             64
  MALE                            102                            186
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.3) MUTATED      10                         9   114
  DEL PEAK 33(19P13.3) WILD-TYPE    32                        12   197
D66V11, multiclass
                           clus
vv                          DEL PEAK 33(19P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              114
                           clus
vv                          DEL PEAK 33(19P13.3) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     6 125
  DEL PEAK 33(19P13.3) WILD-TYPE   3 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      6  125
  DEL PEAK 33(19P13.3) WILD-TYPE    3  227
                        clus
vv                       DEL PEAK 33(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       DEL PEAK 33(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            227
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 34(22Q13.32) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(22Q13.32) MUTATED   102  74
  DEL PEAK 34(22Q13.32) WILD-TYPE 128  79
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            176                             207 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                             74                              79 
$`DEL PEAK 34(22Q13.32) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 
       11.97         8.35        16.27        16.77        27.62         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R 
       41.75        10.22        47.80         2.66        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        5.06         8.35        12.82        17.56        28.70        24.26 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A9FF TCGA-CU-A0YN 
        8.98         1.94        23.01        12.62        11.87        12.92 
TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.19        18.41       130.88         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      123.85        13.58         7.82         8.22        17.72        21.30 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       17.98        67.36        15.68        41.06        38.24        13.58 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
      166.03         8.65         7.53        12.03        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
        0.49        17.39         0.56        12.99         1.22        13.68 
TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 
       12.95        32.02        16.77         8.94        33.04        22.52 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR 
       60.66        24.30        23.41        29.16         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BT 
       12.85        22.98        27.35        20.91        15.58        11.01 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.36         8.25        27.45        18.08         2.70         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK 
       18.81         6.15        12.69        12.36         2.27        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE 
       31.07        17.23         6.48        61.94         7.23        20.12 
TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       17.62        15.91        24.92         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         2.20         7.36        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX 
        7.63        20.05         5.62        10.65        32.98        19.10 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS 
        8.58        19.07        22.72        19.40         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        3.45         9.07        11.70         1.74         1.81        15.42 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
       15.32        15.58        13.48        12.23        16.67        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD 
       17.62        37.05        22.68        86.83        65.75       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF 
       35.24        29.56         4.54         1.64         6.58        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       15.35        48.62         3.22        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG 
       28.24        26.27         2.24         2.10        10.82       110.60 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        7.63         2.96         6.77        98.99        44.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       61.45        86.30        11.97        13.64        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       74.56        13.41         3.48        52.73        52.60        47.84 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       34.06        19.69         8.61        60.16        63.02        35.41 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

$`DEL PEAK 34(22Q13.32) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        91.63       103.50       105.70        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       17.16        34.98        49.12        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       33.83        40.08         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       13.15        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        9.96        28.41         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.34        11.34        13.08         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
       15.62        87.32         2.20        50.27        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 
       76.60        30.67        15.02        12.36        10.49        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       43.50        10.62        38.83        24.66         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
       16.70         0.66        14.56        13.97        14.33         0.92 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.07        15.32        14.37         8.09         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X 
       27.98        17.98        25.74        46.78        14.96         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O 
       26.73        53.88        19.33         5.69        58.92         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
       13.35        62.86         3.06         4.31         9.67         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94         3.25        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       35.24        33.01        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40         2.24        15.81         4.50        14.07        17.75 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATQ 
        3.12        20.98        10.92        27.09         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV 
       27.35         1.51        38.60         3.06         9.01        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A8JT 
        2.76         9.14        27.68         6.38        11.80        21.07 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P 
       14.24         1.84         3.75        12.43        76.01        67.79 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH 
        3.58        17.82        45.04        97.45       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9T2 
       17.88        64.80        79.66        66.41        12.76        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27        66.64        13.74        92.98        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       71.57        91.73         8.32        30.94        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       18.81         3.88        18.84         9.63         0.66        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL 
        7.36        21.11        24.13        30.28        27.19        82.49 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
       20.22         2.89        59.38        38.73        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
        8.52        47.15         5.52 

  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                           0.49                            0.10 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                         166.03                          140.81 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                          15.50                           16.14 
[1] "0.5 - 166.0 (15.5)" "0.1 - 140.8 (16.1)"
[1] "hr=" "1.2"
D67V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 34(22Q13.32) MUTATED         0       50        58       68
  DEL PEAK 34(22Q13.32) WILD-TYPE       4       74        69       61
D67V3, multiclass
           clus
vv          DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  STAGE I                               0                               4
  STAGE II                             50                              74
  STAGE III                            58                              69
  STAGE IV                             68                              61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  DEL PEAK 34(22Q13.32) MUTATED         48 87 27
  DEL PEAK 34(22Q13.32) WILD-TYPE       73 97 26
D67V4, multiclass
          clus
vv         DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  T0+T1+T2                            48                              73
  T3                                  87                              97
  T4                                  27                              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 34(22Q13.32) MUTATED    91  19  46   4
  DEL PEAK 34(22Q13.32) WILD-TYPE 133  23  29   4
D67V5, multiclass
    clus
vv   DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  N0                            91                             133
  N1                            19                              23
  N2                            46                              29
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED    61   4
  DEL PEAK 34(22Q13.32) WILD-TYPE 124   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED     61    4
  DEL PEAK 34(22Q13.32) WILD-TYPE  124    6
   clus
vv  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  0                            61                             124
  1                             4                               6
[1] 2 2
[1] FALSE
D67V7, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED    45 132
  DEL PEAK 34(22Q13.32) WILD-TYPE  56 156
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED     45  132
  DEL PEAK 34(22Q13.32) WILD-TYPE   56  156
        clus
vv       DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  FEMALE                            45                              56
  MALE                             132                             156
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(22Q13.32) MUTATED      12                        12   146
  DEL PEAK 34(22Q13.32) WILD-TYPE    30                         9   165
D67V11, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.32) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               146
                           clus
vv                          DEL PEAK 34(22Q13.32) WILD-TYPE
  ASIAN                                                  30
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                 165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED     6 159
  DEL PEAK 34(22Q13.32) WILD-TYPE   3 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED      6  159
  DEL PEAK 34(22Q13.32) WILD-TYPE    3  193
                        clus
vv                       DEL PEAK 34(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           159
                        clus
vv                       DEL PEAK 34(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             193
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 35(XP11.3) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 35(XP11.3) MUTATED    51  34
  DEL PEAK 35(XP11.3) WILD-TYPE 179 119
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           85                           298 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           34                           119 
$`DEL PEAK 35(XP11.3) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7S 
       91.63       105.70         8.35        16.27        16.83        34.98 
TCGA-4Z-AA84 TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A3PH 
       15.12         2.66        17.88        14.89         5.06         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX 
       17.56        24.26         0.69        12.62        12.10        11.34 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
       12.92         5.19         2.14        19.00        16.70       112.44 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B2 
       15.62        87.32        50.27        21.30         9.67        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A2PC 
       41.06        38.24        13.58       166.03         8.65        43.59 
TCGA-E7-A3X6 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SN 
       24.66         0.92         1.22        16.77        33.04        29.16 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA 
       19.79        12.85        15.58         8.25         2.70        62.86 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3F 
        6.15         2.27        26.93         7.23        17.62        19.46 
TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OF 
        0.49        20.98        19.10         8.48        10.59         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 
        9.01        25.02         1.74         1.81        11.80        15.58 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       12.23         3.75        76.01        67.79         3.58       112.83 
TCGA-XF-A8HF TCGA-XF-A9SZ TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
       97.12        28.24        13.74         7.63         2.96         8.32 
TCGA-XF-AAN1 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA51 TCGA-ZF-AA56 
       30.94        28.41        82.49        34.06        38.73         8.52 
TCGA-ZF-AA58 
       47.15 

$`DEL PEAK 35(XP11.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       22.29        11.97       103.50        44.94        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       10.22        47.80        33.83        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
       16.18        20.48        12.82         9.96        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.87        13.08         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
      130.88        16.14        17.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P 
       64.18        41.56        76.60        67.36        30.67        15.02 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36        10.49         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        15.35        38.83         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       12.99        14.33        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37         8.09        32.02         8.94         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        25.74        46.78        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.36         5.69        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        13.35        18.81        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        35.24        33.01        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.28        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       19.40        38.60         8.22         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
        9.14        27.68         9.07        11.70        15.42         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        21.07        13.48        16.67        14.24         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX 
      110.60        11.31        54.90        71.57        91.73         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        56.48        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.81         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       52.73        52.60        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        63.02        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40        19.17         5.52        10.13 

  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                       166.03                        140.81 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                        15.62                         15.86 
[1] "0.5 - 166.0 (15.6)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1"  
D68V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 35(XP11.3) MUTATED         0       27        30       28
  DEL PEAK 35(XP11.3) WILD-TYPE       4       97        97      101
D68V3, multiclass
           clus
vv          DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  STAGE I                             0                             4
  STAGE II                           27                            97
  STAGE III                          30                            97
  STAGE IV                           28                           101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 35(XP11.3) MUTATED         23  42  14
  DEL PEAK 35(XP11.3) WILD-TYPE       98 142  39
D68V4, multiclass
          clus
vv         DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  T0+T1+T2                          23                            98
  T3                                42                           142
  T4                                14                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 35(XP11.3) MUTATED    50  12  14   2
  DEL PEAK 35(XP11.3) WILD-TYPE 174  30  61   6
D68V5, multiclass
    clus
vv   DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  N0                          50                           174
  N1                          12                            30
  N2                          14                            61
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    42   2
  DEL PEAK 35(XP11.3) WILD-TYPE 143   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     42    2
  DEL PEAK 35(XP11.3) WILD-TYPE  143    8
   clus
vv  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  0                          42                           143
  1                           2                             8
[1] 2 2
[1] FALSE
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    23  64
  DEL PEAK 35(XP11.3) WILD-TYPE  78 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     23   64
  DEL PEAK 35(XP11.3) WILD-TYPE   78  224
        clus
vv       DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  FEMALE                          23                            78
  MALE                            64                           224
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XP11.3) MUTATED       8                         7    69
  DEL PEAK 35(XP11.3) WILD-TYPE    34                        14   242
D68V11, multiclass
                           clus
vv                          DEL PEAK 35(XP11.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              69
                           clus
vv                          DEL PEAK 35(XP11.3) WILD-TYPE
  ASIAN                                                34
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED     1  79
  DEL PEAK 35(XP11.3) WILD-TYPE   8 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED      1   79
  DEL PEAK 35(XP11.3) WILD-TYPE    8  273
                        clus
vv                       DEL PEAK 35(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       DEL PEAK 35(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           273
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 36(XQ21.33) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(XQ21.33) MUTATED    56  26
  DEL PEAK 36(XQ21.33) WILD-TYPE 174 127
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            82                            301 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            26                            127 
$`DEL PEAK 36(XQ21.33) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-BT-A20T 
       91.63       103.50       105.70        16.83         0.62        14.89 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.25        16.18         4.67        17.56        28.70 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CU-A3KJ 
        0.43         0.69        12.62        12.10        11.34         5.46 
TCGA-CU-A3QU TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A6B5 
        5.19        16.70       130.88        50.27        21.30        41.06 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        12.36         8.65        13.64        12.03        43.59 
TCGA-E7-A3X6 TCGA-E7-A7DU TCGA-E7-A85H TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SS 
       24.66         0.92        12.95        16.77        29.16        12.85 
TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB 
        8.25        62.86        31.07         3.25        26.93         7.23 
TCGA-G2-AA3B TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW 
       66.02         0.49         8.94         2.20        10.92        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WV 
       19.10         8.48        10.59        19.07        38.60        21.24 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       27.68         1.74        11.80        15.58        13.48        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
        1.84         3.75        76.01        67.79       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG 
        1.64        17.88        28.24        66.64        13.74       110.60 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        2.96         6.77        18.81        11.97         7.36        21.11 
TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA5H 
       28.41        82.49        47.84        19.17 

$`DEL PEAK 36(XQ21.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       22.29        11.97         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        34.98        27.62        49.12        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 
       66.54        15.12        10.22        47.80        33.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         8.35        17.16        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       24.26        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        18.41        19.00       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
        2.20        13.58         7.82         8.22        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        15.68        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 
       38.24        15.02       166.03        10.49         7.53        43.50 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       10.62        15.35        38.83         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       12.99        14.33         1.22        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37         8.09        32.02         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       17.98         5.52        25.74        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        10.85         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        8.94         6.48        61.94        30.61        15.95        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       33.01        20.12        17.62         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       14.27        19.82        20.28        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
        3.45         2.76         9.14         9.07        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X 
       15.42         6.38        15.32        21.07        16.67        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB 
       65.75         3.58        35.24        29.56         4.54        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27         2.10        92.98        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ 
        7.63        71.57        91.73         8.32        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        13.64        18.64 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        27.19        21.86        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        52.73        52.60        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       35.41        57.90        19.40         8.52        47.15         5.52 
TCGA-ZF-AA5P 
       10.13 

  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                          0.43                           0.10 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                        15.235                         15.810 
[1] "0.4 - 130.9 (15.2)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1.3"
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 36(XQ21.33) MUTATED         0       31        23       25
  DEL PEAK 36(XQ21.33) WILD-TYPE       4       93       104      104
D69V3, multiclass
           clus
vv          DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  STAGE I                              0                              4
  STAGE II                            31                             93
  STAGE III                           23                            104
  STAGE IV                            25                            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 36(XQ21.33) MUTATED         28  36  10
  DEL PEAK 36(XQ21.33) WILD-TYPE       93 148  43
D69V4, multiclass
          clus
vv         DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  T0+T1+T2                           28                             93
  T3                                 36                            148
  T4                                 10                             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"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 36(XQ21.33) MUTATED    51   9  15   1
  DEL PEAK 36(XQ21.33) WILD-TYPE 173  33  60   7
D69V5, multiclass
    clus
vv   DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  N0                           51                            173
  N1                            9                             33
  N2                           15                             60
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    38   0
  DEL PEAK 36(XQ21.33) WILD-TYPE 147  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     38    0
  DEL PEAK 36(XQ21.33) WILD-TYPE  147   10
   clus
vv  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  0                           38                            147
  1                            0                             10
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    24  58
  DEL PEAK 36(XQ21.33) WILD-TYPE  77 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     24   58
  DEL PEAK 36(XQ21.33) WILD-TYPE   77  230
        clus
vv       DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  FEMALE                           24                             77
  MALE                             58                            230
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(XQ21.33) MUTATED       6                         7    66
  DEL PEAK 36(XQ21.33) WILD-TYPE    36                        14   245
D69V11, multiclass
                           clus
vv                          DEL PEAK 36(XQ21.33) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               66
                           clus
vv                          DEL PEAK 36(XQ21.33) WILD-TYPE
  ASIAN                                                 36
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED     4  73
  DEL PEAK 36(XQ21.33) WILD-TYPE   5 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED      4   73
  DEL PEAK 36(XQ21.33) WILD-TYPE    5  279
                        clus
vv                       DEL PEAK 36(XQ21.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           73
                        clus
vv                       DEL PEAK 36(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE
