[1] "ofn"        "-oTSARC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/22507207/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/22534094/transformed.cor.cli.txt"

nPatients in clinical file=261, in cluster file=257, common to both=257
[1]  69 257
[1] "AMP PEAK  1(1P32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           94                           163 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           94                           163 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          105                           152 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          105                           152 
[1] "AMP PEAK  3(1Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                          102                           155 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                          102                           155 
[1] "AMP PEAK  4(2P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           64                           193 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           64                           193 
[1] "AMP PEAK  5(3P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           69                           188 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           69                           188 
[1] "AMP PEAK  6(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         78                         179 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         78                         179 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           119                            138 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           119                            138 
[1] "AMP PEAK  8(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           60                           197 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           60                           197 
[1] "AMP PEAK  9(6Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           75                           182 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           75                           182 
[1] "AMP PEAK 10(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           77                           180 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           77                           180 
[1] "AMP PEAK 11(8P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            81                            176 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            81                            176 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            83                            174 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            83                            174 
[1] "AMP PEAK 13(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            36                            221 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            36                            221 
[1] "AMP PEAK 14(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          94                          163 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          94                          163 
[1] "AMP PEAK 15(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          54                          203 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          54                          203 
[1] "AMP PEAK 16(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            84                            173 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            84                            173 
[1] "AMP PEAK 17(17P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                         102                          155 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                         102                          155 
[1] "AMP PEAK 18(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                           104                            153 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                           104                            153 
[1] "AMP PEAK 19(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            79                            178 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            79                            178 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           108                            149 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           108                            149 
[1] "AMP PEAK 21(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          93                          164 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          93                          164 
[1] "AMP PEAK 22(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             98                             159 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             98                             159 
[1] "AMP PEAK 23(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            73                            184 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            73                            184 
[1] "AMP PEAK 24(XP21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           97                           160 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           97                           160 
[1] "AMP PEAK 25(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           46                           211 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           46                           211 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            69                            188 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            69                            188 
[1] "DEL PEAK  2(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         80                         177 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         80                         177 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           94                           163 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           94                           163 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          108                           149 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          108                           149 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          110                           147 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          110                           147 
[1] "DEL PEAK  6(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            65                            192 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            65                            192 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            51                            206 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            51                            206 
[1] "DEL PEAK  8(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         54                         203 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         54                         203 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           94                           163 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           94                           163 
[1] "DEL PEAK 10(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            33                            224 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            33                            224 
[1] "DEL PEAK 11(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           81                           176 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           81                           176 
[1] "DEL PEAK 12(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           78                           179 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           78                           179 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           71                           186 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           71                           186 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           81                           176 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           81                           176 
[1] "DEL PEAK 15(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                          100                           157 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                          100                           157 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          114                           143 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          114                           143 
[1] "DEL PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           61                           196 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           61                           196 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           128                            129 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           128                            129 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            138                             119 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            138                             119 
[1] "DEL PEAK 20(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           132                            125 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           132                            125 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           110                            147 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           110                            147 
[1] "DEL PEAK 22(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                           118                            139 
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                           118                            139 
[1] "DEL PEAK 23(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         123                          134 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         123                          134 
[1] "DEL PEAK 24(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            87                            170 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            87                            170 
[1] "DEL PEAK 25(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                          56                          201 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                          56                          201 
[1] "DEL PEAK 26(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                             70                             187 
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                             70                             187 
[1] "DEL PEAK 27(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                           180                             77 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                           180                             77 
[1] "DEL PEAK 28(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            80                            177 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            80                            177 
[1] "DEL PEAK 29(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            47                            210 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            47                            210 
[1] "DEL PEAK 30(16Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                           130                            127 
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                           130                            127 
[1] "DEL PEAK 31(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           134                            123 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           134                            123 
[1] "DEL PEAK 32(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                           129                            128 
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                           129                            128 
[1] "DEL PEAK 33(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                            81                            176 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                            81                            176 
[1] "DEL PEAK 34(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                            67                            190 
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                            67                            190 
[1] "DEL PEAK 35(18P11.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                             68                             189 
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                             68                             189 
[1] "DEL PEAK 36(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                          86                          171 
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                          86                          171 
[1] "DEL PEAK 37(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                            70                            187 
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                            70                            187 
[1] "DEL PEAK 38(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                            106                             151 
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                            106                             151 
[1] "DEL PEAK 39(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                            51                            206 
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                            51                            206 
[1] "DEL PEAK 40(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                            66                            191 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                            66                            191 
[1] "DEL PEAK 41(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                             83                             174 
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                             83                             174 
[1] "DEL PEAK 42(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                           55                           202 
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                           55                           202 
[1] "DEL PEAK 43(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                          114                           143 
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                          114                           143 
[1] "DEL PEAK 44(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                          123                           134 
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                          123                           134 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "HISTOLOGICAL_TYPE"                   
[10] "RESIDUAL_TUMOR"                      
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 257 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=95,	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=156,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=33,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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] "****** SUMMARY ***** "
Output Data has 257 columns, 1 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[7] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=33, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=11, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P32.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P32.1) MUTATED    46  48
  AMP PEAK  1(1P32.1) WILD-TYPE 113  50
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           94                           163 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           48                            50 
$`AMP PEAK  1(1P32.1) MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W 
       34.36        15.22        17.95        14.07        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB36 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-KF-A41W 
       13.28        60.00        32.15        37.02        52.11        11.70 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL 
       17.75         6.35        17.52        26.17        35.08        19.69 
TCGA-3B-A9HS TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A23T 
       44.91        18.64        26.56         0.56        18.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LT 
       76.41        66.87         6.28         8.58         9.70        49.05 
TCGA-DX-A3LU TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R 
       86.83        51.02        14.99        45.99        24.26        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6YQ TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BK 
        3.06        50.50        16.87        21.30         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
       45.14        40.77        27.95        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-FX-A2QS 
        1.15        17.79        86.10        77.88        50.40        49.15 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       20.32        67.63         4.57         9.80        80.48        19.53 
TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       37.12         1.05        62.17        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-N1-A6IA 
       63.81        35.28        30.31        25.41        21.73         7.36 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       13.08        48.59        35.90        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8Y0 
       25.35         8.61        10.72        11.93        38.27        22.62 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-Z4-AAPG 
       26.43        45.34        20.65        15.98 

$`AMP PEAK  1(1P32.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       14.43        15.85        40.60        22.85       101.98        30.51 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       84.66        16.60        12.62        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
      159.29        22.62         8.28        18.08        20.94       188.15 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       41.49        50.01        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04        32.71        68.61        12.85        45.11        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23Z TCGA-DX-A240 
       85.02        33.53        66.94        74.66        27.81        60.30 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       95.38        79.17         9.04       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       31.86        35.77         4.54        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O 
       50.43        34.88        85.45         9.73        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BH 
       46.03       108.82        59.84        37.58        37.41        26.99 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       41.00        78.28        86.30        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AB2F 
       47.87        38.17       150.35        40.44        19.43        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B 
       15.72        65.98        66.74         9.21       106.55        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       34.88        33.30         0.72         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-KD-A5QT TCGA-MB-A5YA 
        3.91       101.26        53.33       123.78        16.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        37.55        38.63        81.01        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       46.82        18.08        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
       10.52         0.72        16.77        32.75        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WP-A9GB 
       13.41        12.46         4.80        84.79        65.46         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        35.90        18.08        30.84        35.18        19.17 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                       106.45                        188.15 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                       24.805                        34.680 
[1] "0.6 - 106.5 (24.8)" "0.5 - 188.2 (34.7)"
[1] "hr=" "2.2"
D1V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  1(1P32.1) MUTATED                0                  4
  AMP PEAK  1(1P32.1) WILD-TYPE              1                  3
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  1(1P32.1) MUTATED                     0                   0
  AMP PEAK  1(1P32.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  1(1P32.1) MUTATED                               0
  AMP PEAK  1(1P32.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  1(1P32.1) MUTATED                       0                      8
  AMP PEAK  1(1P32.1) WILD-TYPE                     1                     20
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  1(1P32.1) MUTATED                      1                    0
  AMP PEAK  1(1P32.1) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  1(1P32.1) MUTATED                                       0
  AMP PEAK  1(1P32.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  1(1P32.1) MUTATED                                  0
  AMP PEAK  1(1P32.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  1(1P32.1) MUTATED                                                1
  AMP PEAK  1(1P32.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  1(1P32.1) MUTATED                                 4
  AMP PEAK  1(1P32.1) WILD-TYPE                               6
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  1(1P32.1) MUTATED                                         0
  AMP PEAK  1(1P32.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  1(1P32.1) MUTATED                              0
  AMP PEAK  1(1P32.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  1(1P32.1) MUTATED                         1
  AMP PEAK  1(1P32.1) WILD-TYPE                       1
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  1(1P32.1) MUTATED                                  9
  AMP PEAK  1(1P32.1) WILD-TYPE                                8
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  1(1P32.1) MUTATED                                         4
  AMP PEAK  1(1P32.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  1(1P32.1) MUTATED                             27
  AMP PEAK  1(1P32.1) WILD-TYPE                           17
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  1(1P32.1) MUTATED                                         0
  AMP PEAK  1(1P32.1) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  1(1P32.1) MUTATED                                           0
  AMP PEAK  1(1P32.1) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  1(1P32.1) MUTATED                                                  0
  AMP PEAK  1(1P32.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  1(1P32.1) MUTATED                                          2
  AMP PEAK  1(1P32.1) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  1(1P32.1) MUTATED                                                         1
  AMP PEAK  1(1P32.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  1(1P32.1) MUTATED                                            1
  AMP PEAK  1(1P32.1) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  1(1P32.1) MUTATED                                                  23
  AMP PEAK  1(1P32.1) WILD-TYPE                                                50
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  1(1P32.1) MUTATED                                                    0
  AMP PEAK  1(1P32.1) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  1(1P32.1) MUTATED                                    1
  AMP PEAK  1(1P32.1) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  1(1P32.1) MUTATED                          0
  AMP PEAK  1(1P32.1) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  1(1P32.1) MUTATED                             1
  AMP PEAK  1(1P32.1) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  1(1P32.1) MUTATED                           0
  AMP PEAK  1(1P32.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  1(1P32.1) MUTATED                                   3
  AMP PEAK  1(1P32.1) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  1(1P32.1) MUTATED                                   2
  AMP PEAK  1(1P32.1) WILD-TYPE                                 3
D1V3, multiclass
                                                         clus
vv                                                        AMP PEAK  1(1P32.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                4
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            8
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                23
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        AMP PEAK  1(1P32.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             20
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  50
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P32.1) MUTATED   46 48
  AMP PEAK  1(1P32.1) WILD-TYPE 93 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED     46   48
  AMP PEAK  1(1P32.1) WILD-TYPE   93   70
        clus
vv       AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE
  FEMALE                          46                            93
  MALE                            48                            70
[1] 2 2
[1] FALSE
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P32.1) MUTATED    58  36
  AMP PEAK  1(1P32.1) WILD-TYPE 121  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED     58   36
  AMP PEAK  1(1P32.1) WILD-TYPE  121   36
     clus
vv    AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE
  NO                           58                           121
  YES                          36                            36
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  1(1P32.1) MUTATED                             20             0
  AMP PEAK  1(1P32.1) WILD-TYPE                           39             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  1(1P32.1) MUTATED                                                                          0
  AMP PEAK  1(1P32.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  1(1P32.1) MUTATED                     30
  AMP PEAK  1(1P32.1) WILD-TYPE                   73
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  1(1P32.1) MUTATED                                                  2
  AMP PEAK  1(1P32.1) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  1(1P32.1) MUTATED                 12
  AMP PEAK  1(1P32.1) WILD-TYPE               12
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  1(1P32.1) MUTATED                                                         19
  AMP PEAK  1(1P32.1) WILD-TYPE                                                        9
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  1(1P32.1) MUTATED                                          0
  AMP PEAK  1(1P32.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  1(1P32.1) MUTATED                             0
  AMP PEAK  1(1P32.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  1(1P32.1) MUTATED                               0
  AMP PEAK  1(1P32.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  1(1P32.1) MUTATED                                           11
  AMP PEAK  1(1P32.1) WILD-TYPE                                         10
D1V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  1(1P32.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      20
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              30
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        11
                                                                          clus
vv                                                                         AMP PEAK  1(1P32.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        39
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                73
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          10
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P32.1) MUTATED    50  30   3  11
  AMP PEAK  1(1P32.1) WILD-TYPE 102  39   6  15
D1V7, multiclass
    clus
vv   AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE
  R0                          50                           102
  R1                          30                            39
  R2                           3                             6
  RX                          11                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P32.1) MUTATED       0                         8    81
  AMP PEAK  1(1P32.1) WILD-TYPE     6                        10   143
D1V8, multiclass
                           clus
vv                          AMP PEAK  1(1P32.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              81
                           clus
vv                          AMP PEAK  1(1P32.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P32.1) MUTATED     0  86
  AMP PEAK  1(1P32.1) WILD-TYPE   5 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED      0   86
  AMP PEAK  1(1P32.1) WILD-TYPE    5  134
                        clus
vv                       AMP PEAK  1(1P32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       AMP PEAK  1(1P32.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           134
[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   60 45
  AMP PEAK  2(1Q21.3) WILD-TYPE 99 53
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          105                           152 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           45                            53 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2W 
       31.53        34.68        67.20        34.36        17.95       106.45 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HS-A5N9 
       13.28        30.51        84.66        32.15        37.02        52.11 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-QC-A6FX 
       26.93        28.21        22.62        11.70        17.75        20.94 
TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS 
       17.52        26.17        50.01        19.69        53.49        44.91 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1L2 
       42.84        18.64        26.56         0.56        12.85        85.02 
TCGA-DX-A3LT TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD 
       49.05        35.77        51.02        14.99        10.68        50.43 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 
       85.45        45.99        35.28        52.77        26.47        15.95 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BK 
       78.28        50.50        16.87        34.49         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       45.14        40.77       150.35        27.95        36.69        60.66 
TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS 
        1.15        86.10        66.74       106.55        50.40        49.15 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-HS-A5N8 
       20.32        19.89         8.05        67.63        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
        9.80        80.48        19.53        19.89        25.22       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU 
        5.92        16.41         1.05        62.17       123.78        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VC 
       21.73         7.36        38.63        13.08        17.65        35.90 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB 
       13.41        84.79        38.27        22.62         8.58        18.08 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 
       45.34        35.18        20.65 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        16.18        75.32        15.22        14.43        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       15.85        40.60        12.07        22.85       101.98        60.00 
TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-MB-A5Y9 TCGA-PC-A5DM 
       16.60        12.62        52.27       159.29         8.28         6.35 
TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HQ TCGA-3B-A9HR 
       18.08       188.15        41.49        35.08        68.55        88.57 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        14.37        10.32        38.47        36.03 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        32.71        68.61        45.11        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
       31.86         4.54        73.87        68.55        34.88         9.73 
TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       24.26        46.03       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
        3.06        41.00        86.30        64.21       101.23        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       47.87        38.17        40.44        19.43         6.58        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B 
       12.00        15.72        65.98         9.21        77.88        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A3YV 
       71.31        31.13        21.70        15.48        34.88         4.57 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J 
        3.22         1.38        37.12        13.58        85.97         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
      101.26        53.33        17.36         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57        10.45       122.96        37.55 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
       81.01         1.84        46.82        18.08        48.59        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        10.72        12.46        11.93         4.80 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 
       65.46        63.35        26.43        35.90        30.84        19.17 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       171.09                        188.15 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        30.31                         31.91 
[1] "0.6 - 171.1 (30.3)" "0.5 - 188.2 (31.9)"
[1] "hr=" "1.3"
D2V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  2(1Q21.3) MUTATED                0                  4
  AMP PEAK  2(1Q21.3) WILD-TYPE              1                  3
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  2(1Q21.3) MUTATED                     1                   0
  AMP PEAK  2(1Q21.3) WILD-TYPE                   1                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  2(1Q21.3) MUTATED                               0
  AMP PEAK  2(1Q21.3) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  2(1Q21.3) MUTATED                       0                     19
  AMP PEAK  2(1Q21.3) WILD-TYPE                     1                      9
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  2(1Q21.3) MUTATED                      1                    0
  AMP PEAK  2(1Q21.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  2(1Q21.3) MUTATED                                       0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  2(1Q21.3) MUTATED                                  0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  2(1Q21.3) MUTATED                                                1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  2(1Q21.3) MUTATED                                 2
  AMP PEAK  2(1Q21.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  2(1Q21.3) MUTATED                                         0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  2(1Q21.3) MUTATED                              1
  AMP PEAK  2(1Q21.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  2(1Q21.3) MUTATED                         0
  AMP PEAK  2(1Q21.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  2(1Q21.3) MUTATED                                 11
  AMP PEAK  2(1Q21.3) WILD-TYPE                                6
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  2(1Q21.3) MUTATED                                         2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  2(1Q21.3) MUTATED                             23
  AMP PEAK  2(1Q21.3) WILD-TYPE                           21
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  2(1Q21.3) MUTATED                                         1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  2(1Q21.3) MUTATED                                           1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  2(1Q21.3) MUTATED                                                  1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  2(1Q21.3) MUTATED                                          2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  2(1Q21.3) MUTATED                                                         1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  2(1Q21.3) MUTATED                                            1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  2(1Q21.3) MUTATED                                                  22
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                51
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  2(1Q21.3) MUTATED                                                    0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  2(1Q21.3) MUTATED                                    0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  2(1Q21.3) MUTATED                          2
  AMP PEAK  2(1Q21.3) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  2(1Q21.3) MUTATED                             2
  AMP PEAK  2(1Q21.3) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  2(1Q21.3) MUTATED                           0
  AMP PEAK  2(1Q21.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  2(1Q21.3) MUTATED                                   3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  2(1Q21.3) MUTATED                                   3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                 2
D2V3, multiclass
                                                         clus
vv                                                        AMP PEAK  2(1Q21.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                4
  CHEST - LUNG/PLEURA                                                               1
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           19
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                 11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        AMP PEAK  2(1Q21.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 1
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                              9
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  51
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   64 41
  AMP PEAK  2(1Q21.3) WILD-TYPE 75 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     64   41
  AMP PEAK  2(1Q21.3) WILD-TYPE   75   77
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          64                            75
  MALE                            41                            77
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    66  37
  AMP PEAK  2(1Q21.3) WILD-TYPE 113  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     66   37
  AMP PEAK  2(1Q21.3) WILD-TYPE  113   35
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           66                           113
  YES                          37                            35
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  2(1Q21.3) MUTATED                             16             0
  AMP PEAK  2(1Q21.3) WILD-TYPE                           43             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  2(1Q21.3) MUTATED                                                                          0
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  2(1Q21.3) MUTATED                     45
  AMP PEAK  2(1Q21.3) WILD-TYPE                   58
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  2(1Q21.3) MUTATED                                                  3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                6
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  2(1Q21.3) MUTATED                 10
  AMP PEAK  2(1Q21.3) WILD-TYPE               14
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  2(1Q21.3) MUTATED                                                         18
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                       10
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  2(1Q21.3) MUTATED                                          1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        1
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  2(1Q21.3) MUTATED                             0
  AMP PEAK  2(1Q21.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  2(1Q21.3) MUTATED                               0
  AMP PEAK  2(1Q21.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  2(1Q21.3) MUTATED                                           12
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          9
D2V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  2(1Q21.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      16
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              45
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   3
  MYXOFIBROSARCOMA                                                                                  10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        12
                                                                          clus
vv                                                                         AMP PEAK  2(1Q21.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        43
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                58
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     6
  MYXOFIBROSARCOMA                                                                                    14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q21.3) MUTATED   61 25  5 14
  AMP PEAK  2(1Q21.3) WILD-TYPE 91 44  4 12
D2V7, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                          61                            91
  R1                          25                            44
  R2                           5                             4
  RX                          14                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       2                         8    88
  AMP PEAK  2(1Q21.3) WILD-TYPE     4                        10   136
D2V8, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              88
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  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"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     1  88
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      1   88
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  132
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q24.3) MUTATED    56  46
  AMP PEAK  3(1Q24.3) WILD-TYPE 103  52
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                          102                           155 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                           46                            52 
$`AMP PEAK  3(1Q24.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB35 TCGA-HB-A43Z TCGA-HB-A5W3 
       34.68        34.36        17.95        30.51        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-SG-A849 TCGA-X6-A8C6 
       52.11        26.93        22.62        17.75        17.52        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I3 
       50.01        19.69        53.49        44.91        42.84        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
        0.56        14.04        12.85        18.54        85.02        33.53 
TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U6 TCGA-DX-A3U7 
       76.41        60.30         9.70        49.05        35.77        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       14.99        50.43        85.45        45.99        35.28        52.77 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       26.47        15.95        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       41.00        78.28        34.49         9.34        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       47.87        40.77       150.35        27.95        36.69        60.66 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G 
       86.10        66.74         9.21        49.15        20.32        19.89 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        8.05        67.63        34.88         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VF 
       19.53        19.89        37.12        25.22       171.09         1.05 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-MB-A5Y8 
       62.17       123.78        23.38         5.19        63.81        25.41 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5VC TCGA-QQ-A8VH 
       21.73         7.36        38.63        13.08        35.90        10.52 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU 
       18.94         3.88        22.82        32.75         8.61        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 
       10.72        12.46        11.93        84.79        38.27        22.62 
TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 
        8.58        18.08        45.34        35.18        20.65        27.32 

$`AMP PEAK  3(1Q24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85       101.98        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 
       16.60        52.27        28.21       159.29        11.70         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT 
        6.35        18.08        20.94       188.15        26.17        41.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       68.55        88.57        54.74        25.25        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       38.47        36.03        18.64        32.71        68.61        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y 
       54.21        66.94        74.66         5.26        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       27.81         8.58        95.38        79.17         9.04        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A3UA 
      136.44        33.44        44.68        31.86         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P 
       73.87        68.55        34.88         9.73        24.26        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       28.96        50.50        16.87        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       20.05        38.17        40.44        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2T TCGA-DX-AB2V 
       17.79        12.00        15.72        65.98        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y 
       50.40        50.89        71.31        31.13        21.70        15.48 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IS-A3KA TCGA-IW-A3M4 
        4.57        33.30         3.22         1.38        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT 
        5.92        16.41         3.91       101.26        53.33        17.36 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       16.41        35.28        30.31         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57        10.45       122.96        37.55 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        64.77         0.72        16.77 
TCGA-SI-A71P TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-X2-A95T 
       25.35        19.63        13.22         4.80        65.46        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       26.43        35.90        30.84        19.17        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                       171.09                        188.15 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                       31.235                        31.130 
[1] "0.6 - 171.1 (31.2)" "0.5 - 188.2 (31.1)"
[1] "hr=" "1.5"
D3V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  3(1Q24.3) MUTATED                0                  5
  AMP PEAK  3(1Q24.3) WILD-TYPE              1                  2
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  3(1Q24.3) MUTATED                     1                   0
  AMP PEAK  3(1Q24.3) WILD-TYPE                   1                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  3(1Q24.3) MUTATED                               1
  AMP PEAK  3(1Q24.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  3(1Q24.3) MUTATED                       0                     14
  AMP PEAK  3(1Q24.3) WILD-TYPE                     1                     14
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  3(1Q24.3) MUTATED                      1                    0
  AMP PEAK  3(1Q24.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  3(1Q24.3) MUTATED                                       0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  3(1Q24.3) MUTATED                                  0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  3(1Q24.3) MUTATED                                                1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  3(1Q24.3) MUTATED                                 3
  AMP PEAK  3(1Q24.3) WILD-TYPE                               7
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  3(1Q24.3) MUTATED                                         1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  3(1Q24.3) MUTATED                              0
  AMP PEAK  3(1Q24.3) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  3(1Q24.3) MUTATED                         0
  AMP PEAK  3(1Q24.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  3(1Q24.3) MUTATED                                  9
  AMP PEAK  3(1Q24.3) WILD-TYPE                                8
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  3(1Q24.3) MUTATED                                         4
  AMP PEAK  3(1Q24.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  3(1Q24.3) MUTATED                             18
  AMP PEAK  3(1Q24.3) WILD-TYPE                           26
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  3(1Q24.3) MUTATED                                         1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  3(1Q24.3) MUTATED                                           1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  3(1Q24.3) MUTATED                                                  0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  3(1Q24.3) MUTATED                                          3
  AMP PEAK  3(1Q24.3) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  3(1Q24.3) MUTATED                                                         1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  3(1Q24.3) MUTATED                                            1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  3(1Q24.3) MUTATED                                                  27
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                46
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  3(1Q24.3) MUTATED                                                    0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  3(1Q24.3) MUTATED                                    0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  3(1Q24.3) MUTATED                          1
  AMP PEAK  3(1Q24.3) WILD-TYPE                        4
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  3(1Q24.3) MUTATED                             1
  AMP PEAK  3(1Q24.3) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  3(1Q24.3) MUTATED                           0
  AMP PEAK  3(1Q24.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  3(1Q24.3) MUTATED                                   4
  AMP PEAK  3(1Q24.3) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  3(1Q24.3) MUTATED                                   4
  AMP PEAK  3(1Q24.3) WILD-TYPE                                 1
D3V3, multiclass
                                                         clus
vv                                                        AMP PEAK  3(1Q24.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                5
  CHEST - LUNG/PLEURA                                                               1
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           14
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 4
                                                         clus
vv                                                        AMP PEAK  3(1Q24.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 1
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             14
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q24.3) MUTATED   56 46
  AMP PEAK  3(1Q24.3) WILD-TYPE 83 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q24.3) MUTATED     56   46
  AMP PEAK  3(1Q24.3) WILD-TYPE   83   72
        clus
vv       AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE
  FEMALE                          56                            83
  MALE                            46                            72
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q24.3) MUTATED    65  37
  AMP PEAK  3(1Q24.3) WILD-TYPE 114  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q24.3) MUTATED     65   37
  AMP PEAK  3(1Q24.3) WILD-TYPE  114   35
     clus
vv    AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE
  NO                           65                           114
  YES                          37                            35
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  3(1Q24.3) MUTATED                             24             0
  AMP PEAK  3(1Q24.3) WILD-TYPE                           35             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  3(1Q24.3) MUTATED                                                                          0
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  3(1Q24.3) MUTATED                     39
  AMP PEAK  3(1Q24.3) WILD-TYPE                   64
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  3(1Q24.3) MUTATED                                                  3
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                6
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  3(1Q24.3) MUTATED                  9
  AMP PEAK  3(1Q24.3) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  3(1Q24.3) MUTATED                                                         14
  AMP PEAK  3(1Q24.3) WILD-TYPE                                                       14
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  3(1Q24.3) MUTATED                                          1
  AMP PEAK  3(1Q24.3) WILD-TYPE                                        1
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  3(1Q24.3) MUTATED                             0
  AMP PEAK  3(1Q24.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  3(1Q24.3) MUTATED                               0
  AMP PEAK  3(1Q24.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  3(1Q24.3) MUTATED                                           12
  AMP PEAK  3(1Q24.3) WILD-TYPE                                          9
D3V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  3(1Q24.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      24
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              39
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   3
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        12
                                                                          clus
vv                                                                         AMP PEAK  3(1Q24.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        35
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                64
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     6
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(1Q24.3) MUTATED   57 30  5 10
  AMP PEAK  3(1Q24.3) WILD-TYPE 95 39  4 16
D3V7, multiclass
    clus
vv   AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE
  R0                          57                            95
  R1                          30                            39
  R2                           5                             4
  RX                          10                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q24.3) MUTATED       2                         5    90
  AMP PEAK  3(1Q24.3) WILD-TYPE     4                        13   134
D3V8, multiclass
                           clus
vv                          AMP PEAK  3(1Q24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              90
                           clus
vv                          AMP PEAK  3(1Q24.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            13
  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"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q24.3) MUTATED     2  89
  AMP PEAK  3(1Q24.3) WILD-TYPE   3 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q24.3) MUTATED      2   89
  AMP PEAK  3(1Q24.3) WILD-TYPE    3  131
                        clus
vv                       AMP PEAK  3(1Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       AMP PEAK  3(1Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           131
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P11.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P11.2) MUTATED    36  28
  AMP PEAK  4(2P11.2) WILD-TYPE 123  70
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           64                           193 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           28                            70 
$`AMP PEAK  4(2P11.2) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X 
       34.68        34.36        17.95        12.07       106.45        13.28 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-KF-A41W 
       84.66        32.15        37.02        52.27        22.62        11.70 
TCGA-QQ-A8VB TCGA-X6-A8C6 TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I3 
      188.15        35.08        25.25        42.84        10.32        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT 
       14.04        32.71        18.54        74.66         6.28        49.05 
TCGA-DX-A3U7 TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A6BA 
       51.02        68.55        85.45        45.99        24.26        82.68 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ 
       78.28        50.50        86.30        21.30        34.49         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2Q 
       61.97        45.14        38.17         6.58        86.10        66.74 
TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3KA 
       50.40        49.15         4.57         3.22        37.12        13.58 
TCGA-IW-A3M5 TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DL 
        5.92        63.81        16.41        21.73        10.45        37.55 
TCGA-PC-A5DO TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS 
       81.01         3.88        25.35        13.41        10.72        84.79 
TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       26.43        20.65        15.95        15.98 

$`AMP PEAK  4(2P11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 
       14.43        14.07        15.85        40.60        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       30.51        60.00        16.60        12.62        52.11        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21       159.29        17.75         8.28         6.35        18.08 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94        17.52        26.17        41.49        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV 
       53.49        68.55        88.57        44.91        54.74        14.37 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY 
       38.47        36.03        18.64         0.56        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       45.11        54.21        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       44.68        31.86        35.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O 
       73.87        50.43        34.88         9.73        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM 
        3.06        41.00        16.87        64.21       101.23        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BM 
       30.35       152.12        29.49        48.20        20.05        47.87 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       40.77       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
        9.21        77.88       106.55        50.89        71.31        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE 
        1.38        19.89        25.22       171.09        85.97        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
       17.36        23.38         5.19        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        22.39        11.57 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        7.36       122.96        38.63        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-AB3D 
       22.82        32.75         8.61        19.63        13.22        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       11.93         4.80        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        35.90        18.08        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC 
       13.38 

  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                         3.22                          0.49 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                       188.15                        171.09 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                       33.535                        30.510 
[1] "3.2 - 188.2 (33.5)" "0.5 - 171.1 (30.5)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  4(2P11.2) MUTATED                0                  2
  AMP PEAK  4(2P11.2) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  4(2P11.2) MUTATED                     0                   0
  AMP PEAK  4(2P11.2) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  4(2P11.2) MUTATED                               0
  AMP PEAK  4(2P11.2) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  4(2P11.2) MUTATED                       0                      7
  AMP PEAK  4(2P11.2) WILD-TYPE                     1                     21
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  4(2P11.2) MUTATED                      0                    0
  AMP PEAK  4(2P11.2) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  4(2P11.2) MUTATED                                       0
  AMP PEAK  4(2P11.2) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  4(2P11.2) MUTATED                                  0
  AMP PEAK  4(2P11.2) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  4(2P11.2) MUTATED                                                0
  AMP PEAK  4(2P11.2) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  4(2P11.2) MUTATED                                 1
  AMP PEAK  4(2P11.2) WILD-TYPE                               9
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  4(2P11.2) MUTATED                                         0
  AMP PEAK  4(2P11.2) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  4(2P11.2) MUTATED                              0
  AMP PEAK  4(2P11.2) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  4(2P11.2) MUTATED                         0
  AMP PEAK  4(2P11.2) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  4(2P11.2) MUTATED                                  6
  AMP PEAK  4(2P11.2) WILD-TYPE                               11
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  4(2P11.2) MUTATED                                         2
  AMP PEAK  4(2P11.2) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  4(2P11.2) MUTATED                             17
  AMP PEAK  4(2P11.2) WILD-TYPE                           27
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  4(2P11.2) MUTATED                                         1
  AMP PEAK  4(2P11.2) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  4(2P11.2) MUTATED                                           1
  AMP PEAK  4(2P11.2) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  4(2P11.2) MUTATED                                                  1
  AMP PEAK  4(2P11.2) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  4(2P11.2) MUTATED                                          2
  AMP PEAK  4(2P11.2) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  4(2P11.2) MUTATED                                                         1
  AMP PEAK  4(2P11.2) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  4(2P11.2) MUTATED                                            0
  AMP PEAK  4(2P11.2) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  4(2P11.2) MUTATED                                                  16
  AMP PEAK  4(2P11.2) WILD-TYPE                                                57
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  4(2P11.2) MUTATED                                                    0
  AMP PEAK  4(2P11.2) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  4(2P11.2) MUTATED                                    0
  AMP PEAK  4(2P11.2) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  4(2P11.2) MUTATED                          0
  AMP PEAK  4(2P11.2) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  4(2P11.2) MUTATED                             2
  AMP PEAK  4(2P11.2) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  4(2P11.2) MUTATED                           0
  AMP PEAK  4(2P11.2) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  4(2P11.2) MUTATED                                   2
  AMP PEAK  4(2P11.2) WILD-TYPE                                 5
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  4(2P11.2) MUTATED                                   2
  AMP PEAK  4(2P11.2) WILD-TYPE                                 3
D4V3, multiclass
                                                         clus
vv                                                        AMP PEAK  4(2P11.2) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            7
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        AMP PEAK  4(2P11.2) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             21
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P11.2) MUTATED   40 24
  AMP PEAK  4(2P11.2) WILD-TYPE 99 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P11.2) MUTATED     40   24
  AMP PEAK  4(2P11.2) WILD-TYPE   99   94
        clus
vv       AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE
  FEMALE                          40                            99
  MALE                            24                            94
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P11.2) MUTATED    42  20
  AMP PEAK  4(2P11.2) WILD-TYPE 137  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P11.2) MUTATED     42   20
  AMP PEAK  4(2P11.2) WILD-TYPE  137   52
     clus
vv    AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE
  NO                           42                           137
  YES                          20                            52
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  4(2P11.2) MUTATED                             13             0
  AMP PEAK  4(2P11.2) WILD-TYPE                           46             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  4(2P11.2) MUTATED                                                                          0
  AMP PEAK  4(2P11.2) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  4(2P11.2) MUTATED                     23
  AMP PEAK  4(2P11.2) WILD-TYPE                   80
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  4(2P11.2) MUTATED                                                  2
  AMP PEAK  4(2P11.2) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  4(2P11.2) MUTATED                  7
  AMP PEAK  4(2P11.2) WILD-TYPE               17
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  4(2P11.2) MUTATED                                                         12
  AMP PEAK  4(2P11.2) WILD-TYPE                                                       16
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  4(2P11.2) MUTATED                                          1
  AMP PEAK  4(2P11.2) WILD-TYPE                                        1
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  4(2P11.2) MUTATED                             0
  AMP PEAK  4(2P11.2) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  4(2P11.2) MUTATED                               0
  AMP PEAK  4(2P11.2) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  4(2P11.2) MUTATED                                            6
  AMP PEAK  4(2P11.2) WILD-TYPE                                         15
D4V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  4(2P11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      13
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                   7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         6
                                                                          clus
vv                                                                         AMP PEAK  4(2P11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        46
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          15
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(2P11.2) MUTATED    41  15   1   7
  AMP PEAK  4(2P11.2) WILD-TYPE 111  54   8  19
D4V7, multiclass
    clus
vv   AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE
  R0                          41                           111
  R1                          15                            54
  R2                           1                             8
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P11.2) MUTATED       3                         2    58
  AMP PEAK  4(2P11.2) WILD-TYPE     3                        16   166
D4V8, multiclass
                           clus
vv                          AMP PEAK  4(2P11.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              58
                           clus
vv                          AMP PEAK  4(2P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            16
  WHITE                                               166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P11.2) MUTATED     1  58
  AMP PEAK  4(2P11.2) WILD-TYPE   4 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P11.2) MUTATED      1   58
  AMP PEAK  4(2P11.2) WILD-TYPE    4  162
                        clus
vv                       AMP PEAK  4(2P11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK  4(2P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           162
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3P12.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(3P12.1) MUTATED    37  32
  AMP PEAK  5(3P12.1) WILD-TYPE 122  66
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           69                           188 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           32                            66 
$`AMP PEAK  5(3P12.1) MUTATED`
TCGA-DX-A6BK TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P 
       16.18        15.22        17.95        14.43        14.07        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB37 TCGA-IF-A4AK TCGA-KF-A41W 
      106.45        13.28       101.98        84.66        52.27        11.70 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
        6.35        18.08        20.94        17.52        26.17        35.08 
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW 
       19.69        88.57        42.84        18.64         0.56        32.71 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U8 
       74.66         6.28         9.04        49.05        51.02         4.54 
TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A8BL 
       85.45        26.47        78.28        86.30        21.30        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AATS 
       47.87        38.17        27.95        40.44        36.69         1.15 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3TO 
       17.79        15.72        86.10       106.55        50.40        20.32 
TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-K1-A6RU 
       67.63        80.48        19.53         3.22        25.22        23.38 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MJ-A68H TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-SI-AA8B 
       63.81        35.28        14.99        13.08        46.82         8.61 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB 
       13.41        10.72        12.46        84.79        22.62         8.58 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X9-A971 
       26.43        45.34        27.32 

$`AMP PEAK  5(3P12.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        67.20        34.36        75.32 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A 
       15.85        40.60        22.85        30.51        60.00        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 
       16.60        37.02        12.62        52.11        26.93        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QQ-A8VB TCGA-WK-A8XT 
      159.29        22.62        17.75         8.28       188.15        41.49 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       50.01        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU 
       14.37        10.32        38.47        36.03        26.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU 
       60.30         8.58         9.70        95.38        79.17        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      136.44        33.44        44.68        31.86        35.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        73.87        68.55        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       45.99        24.26        35.28        52.77        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM 
       50.50        16.87        64.21       101.23        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       61.97        40.77       150.35        60.66        19.43         6.58 
TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B 
       12.00        65.98        66.74         9.21        77.88        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       71.31        49.15        31.13        21.70        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        19.89        37.12       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I 
       62.17       123.78        17.36         5.19        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       25.41         0.49        21.73        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01        17.65         1.84        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY 
       19.63        13.22        11.93         4.80        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        35.90        18.08        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                       106.55                        188.15 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                       25.220                        33.025 
[1] "0.6 - 106.5 (25.2)" "0.5 - 188.2 (33.0)"
[1] "hr=" "1.4"
D5V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  5(3P12.1) MUTATED                0                  2
  AMP PEAK  5(3P12.1) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  5(3P12.1) MUTATED                     0                   0
  AMP PEAK  5(3P12.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  5(3P12.1) MUTATED                               0
  AMP PEAK  5(3P12.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  5(3P12.1) MUTATED                       0                      5
  AMP PEAK  5(3P12.1) WILD-TYPE                     1                     23
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  5(3P12.1) MUTATED                      1                    0
  AMP PEAK  5(3P12.1) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  5(3P12.1) MUTATED                                       0
  AMP PEAK  5(3P12.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  5(3P12.1) MUTATED                                  0
  AMP PEAK  5(3P12.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  5(3P12.1) MUTATED                                                1
  AMP PEAK  5(3P12.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  5(3P12.1) MUTATED                                 0
  AMP PEAK  5(3P12.1) WILD-TYPE                              10
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  5(3P12.1) MUTATED                                         1
  AMP PEAK  5(3P12.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  5(3P12.1) MUTATED                              0
  AMP PEAK  5(3P12.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  5(3P12.1) MUTATED                         0
  AMP PEAK  5(3P12.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  5(3P12.1) MUTATED                                  4
  AMP PEAK  5(3P12.1) WILD-TYPE                               13
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  5(3P12.1) MUTATED                                         3
  AMP PEAK  5(3P12.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  5(3P12.1) MUTATED                             24
  AMP PEAK  5(3P12.1) WILD-TYPE                           20
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  5(3P12.1) MUTATED                                         1
  AMP PEAK  5(3P12.1) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  5(3P12.1) MUTATED                                           1
  AMP PEAK  5(3P12.1) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  5(3P12.1) MUTATED                                                  0
  AMP PEAK  5(3P12.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  5(3P12.1) MUTATED                                          0
  AMP PEAK  5(3P12.1) WILD-TYPE                                        8
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  5(3P12.1) MUTATED                                                         0
  AMP PEAK  5(3P12.1) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  5(3P12.1) MUTATED                                            0
  AMP PEAK  5(3P12.1) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  5(3P12.1) MUTATED                                                  14
  AMP PEAK  5(3P12.1) WILD-TYPE                                                59
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  5(3P12.1) MUTATED                                                    0
  AMP PEAK  5(3P12.1) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  5(3P12.1) MUTATED                                    2
  AMP PEAK  5(3P12.1) WILD-TYPE                                  0
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  5(3P12.1) MUTATED                          2
  AMP PEAK  5(3P12.1) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  5(3P12.1) MUTATED                             0
  AMP PEAK  5(3P12.1) WILD-TYPE                           4
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  5(3P12.1) MUTATED                           0
  AMP PEAK  5(3P12.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  5(3P12.1) MUTATED                                   5
  AMP PEAK  5(3P12.1) WILD-TYPE                                 2
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  5(3P12.1) MUTATED                                   3
  AMP PEAK  5(3P12.1) WILD-TYPE                                 2
D5V3, multiclass
                                                         clus
vv                                                        AMP PEAK  5(3P12.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            5
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       0
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        AMP PEAK  5(3P12.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             23
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  0
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         4
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P12.1) MUTATED    34  35
  AMP PEAK  5(3P12.1) WILD-TYPE 105  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P12.1) MUTATED     34   35
  AMP PEAK  5(3P12.1) WILD-TYPE  105   83
        clus
vv       AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE
  FEMALE                          34                           105
  MALE                            35                            83
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P12.1) MUTATED    42  26
  AMP PEAK  5(3P12.1) WILD-TYPE 137  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P12.1) MUTATED     42   26
  AMP PEAK  5(3P12.1) WILD-TYPE  137   46
     clus
vv    AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE
  NO                           42                           137
  YES                          26                            46
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  5(3P12.1) MUTATED                             10             0
  AMP PEAK  5(3P12.1) WILD-TYPE                           49             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  5(3P12.1) MUTATED                                                                          0
  AMP PEAK  5(3P12.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  5(3P12.1) MUTATED                     21
  AMP PEAK  5(3P12.1) WILD-TYPE                   82
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  5(3P12.1) MUTATED                                                  0
  AMP PEAK  5(3P12.1) WILD-TYPE                                                9
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  5(3P12.1) MUTATED                  9
  AMP PEAK  5(3P12.1) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  5(3P12.1) MUTATED                                                         18
  AMP PEAK  5(3P12.1) WILD-TYPE                                                       10
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  5(3P12.1) MUTATED                                          0
  AMP PEAK  5(3P12.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  5(3P12.1) MUTATED                             0
  AMP PEAK  5(3P12.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  5(3P12.1) MUTATED                               0
  AMP PEAK  5(3P12.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  5(3P12.1) MUTATED                                           11
  AMP PEAK  5(3P12.1) WILD-TYPE                                         10
D5V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  5(3P12.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      10
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   0
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        11
                                                                          clus
vv                                                                         AMP PEAK  5(3P12.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        49
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     9
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          10
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(3P12.1) MUTATED    41  22   1   5
  AMP PEAK  5(3P12.1) WILD-TYPE 111  47   8  21
D5V7, multiclass
    clus
vv   AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE
  R0                          41                           111
  R1                          22                            47
  R2                           1                             8
  RX                           5                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3P12.1) MUTATED       1                         6    60
  AMP PEAK  5(3P12.1) WILD-TYPE     5                        12   164
D5V8, multiclass
                           clus
vv                          AMP PEAK  5(3P12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              60
                           clus
vv                          AMP PEAK  5(3P12.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P12.1) MUTATED     0  62
  AMP PEAK  5(3P12.1) WILD-TYPE   5 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P12.1) MUTATED      0   62
  AMP PEAK  5(3P12.1) WILD-TYPE    5  158
                        clus
vv                       AMP PEAK  5(3P12.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       AMP PEAK  5(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           158
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(4Q12) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(4Q12) MUTATED    46  32
  AMP PEAK  6(4Q12) WILD-TYPE 113  66
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         78                         179 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         32                          66 
$`AMP PEAK  6(4Q12) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2P 
       34.68        34.36        15.22        17.95        14.43        12.07 
TCGA-DX-AB2W TCGA-HS-A5N9 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QQ-A8VB 
      106.45        52.11        11.70         8.28         6.35       188.15 
TCGA-VT-A80J TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 
       26.17        88.57        44.91        42.84        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
        0.56        68.61        12.85        18.54        54.21        74.66 
TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YR 
       33.44        51.02        45.99        15.95        82.68        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7ES TCGA-DX-A8BJ 
       78.28        50.50        86.30        64.21        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU 
       61.97        45.14        47.87        40.77        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-HB-A3YV TCGA-IE-A4EJ 
       60.66        17.79        12.00        66.74         4.57         3.22 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU 
       19.89       171.09        13.58        23.38         5.19        35.28 
TCGA-LI-A67I TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DO 
       30.31        21.73        14.99        10.45        37.55        81.01 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O 
       13.08        18.08        48.59        16.77        18.94        22.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
        8.61        13.22        13.41        10.72        12.46        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       22.62         8.58        26.43        35.18        15.95        15.98 

$`AMP PEAK  6(4Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BP 
       36.30        31.53        16.18        67.20        75.32        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       15.85        40.60        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        22.62        17.75 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
       18.08        20.94        17.52        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       19.69        53.49        68.55        54.74        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ 
       10.32        38.47        36.03        14.04        32.71        45.11 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       79.17         9.04        49.05        86.83       136.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       68.55        50.43        34.88        85.45         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.58        37.41        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       26.99         3.06        16.87       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BN 
       62.20        30.35       152.12        29.49        48.20        38.17 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2G 
      150.35        40.44        19.43         6.58         1.15        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       65.98        86.10         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
       19.89        15.48         8.05        67.63        34.88        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
        0.72         9.80        80.48        19.53         1.38        37.12 
TCGA-IF-A4AJ TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       25.22        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS 
      101.26        53.33        62.17       123.78        17.36        63.81 
TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       16.41        25.41         0.49        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5V2 
       11.57         7.36       122.96        38.63        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       46.82        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       10.52         0.72         3.88        25.35        32.75        19.63 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
       11.93         4.80        38.27        65.46        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        30.84        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       29.46        27.32        36.43         4.37        13.38 

  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                       0.56                        0.49 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                     188.15                      159.29 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                     24.775                      32.710 
[1] "0.6 - 188.2 (24.8)" "0.5 - 159.3 (32.7)"
[1] "hr=" "1.2"
D6V2, continuous
                             vv
clus                          CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  6(4Q12) MUTATED                0                  4
  AMP PEAK  6(4Q12) WILD-TYPE              1                  3
                             vv
clus                          CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  6(4Q12) MUTATED                     0                   0
  AMP PEAK  6(4Q12) WILD-TYPE                   2                   1
                             vv
clus                          CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  6(4Q12) MUTATED                               0
  AMP PEAK  6(4Q12) WILD-TYPE                             2
                             vv
clus                          GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  6(4Q12) MUTATED                       0                      7
  AMP PEAK  6(4Q12) WILD-TYPE                     1                     21
                             vv
clus                          HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  6(4Q12) MUTATED                      2                    0
  AMP PEAK  6(4Q12) WILD-TYPE                    0                    1
                             vv
clus                          HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  6(4Q12) MUTATED                                       0
  AMP PEAK  6(4Q12) WILD-TYPE                                     2
                             vv
clus                          LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  6(4Q12) MUTATED                                  0
  AMP PEAK  6(4Q12) WILD-TYPE                                1
                             vv
clus                          LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  6(4Q12) MUTATED                                                1
  AMP PEAK  6(4Q12) WILD-TYPE                                              1
                             vv
clus                          LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  6(4Q12) MUTATED                                 2
  AMP PEAK  6(4Q12) WILD-TYPE                               8
                             vv
clus                          LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  6(4Q12) MUTATED                                         0
  AMP PEAK  6(4Q12) WILD-TYPE                                       2
                             vv
clus                          LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  6(4Q12) MUTATED                              0
  AMP PEAK  6(4Q12) WILD-TYPE                            4
                             vv
clus                          LOWER EXTREMITY - GROIN
  AMP PEAK  6(4Q12) MUTATED                         1
  AMP PEAK  6(4Q12) WILD-TYPE                       1
                             vv
clus                          LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  6(4Q12) MUTATED                                  6
  AMP PEAK  6(4Q12) WILD-TYPE                               11
                             vv
clus                          LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  6(4Q12) MUTATED                                         4
  AMP PEAK  6(4Q12) WILD-TYPE                                       1
                             vv
clus                          LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  6(4Q12) MUTATED                             20
  AMP PEAK  6(4Q12) WILD-TYPE                           24
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  6(4Q12) MUTATED                                         1
  AMP PEAK  6(4Q12) WILD-TYPE                                       3
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  6(4Q12) MUTATED                                           1
  AMP PEAK  6(4Q12) WILD-TYPE                                         1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  6(4Q12) MUTATED                                                  1
  AMP PEAK  6(4Q12) WILD-TYPE                                                4
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  6(4Q12) MUTATED                                          1
  AMP PEAK  6(4Q12) WILD-TYPE                                        7
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  6(4Q12) MUTATED                                                         0
  AMP PEAK  6(4Q12) WILD-TYPE                                                       2
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  6(4Q12) MUTATED                                            0
  AMP PEAK  6(4Q12) WILD-TYPE                                          1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  6(4Q12) MUTATED                                                  16
  AMP PEAK  6(4Q12) WILD-TYPE                                                57
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  6(4Q12) MUTATED                                                    0
  AMP PEAK  6(4Q12) WILD-TYPE                                                  3
                             vv
clus                          SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  6(4Q12) MUTATED                                    2
  AMP PEAK  6(4Q12) WILD-TYPE                                  0
                             vv
clus                          SUPERFICIAL TRUNK - BACK
  AMP PEAK  6(4Q12) MUTATED                          0
  AMP PEAK  6(4Q12) WILD-TYPE                        5
                             vv
clus                          SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  6(4Q12) MUTATED                             2
  AMP PEAK  6(4Q12) WILD-TYPE                           2
                             vv
clus                          SUPERFICIAL TRUNK - FLANK
  AMP PEAK  6(4Q12) MUTATED                           0
  AMP PEAK  6(4Q12) WILD-TYPE                         1
                             vv
clus                          UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  6(4Q12) MUTATED                                   5
  AMP PEAK  6(4Q12) WILD-TYPE                                 2
                             vv
clus                          UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  6(4Q12) MUTATED                                   2
  AMP PEAK  6(4Q12) WILD-TYPE                                 3
D6V3, multiclass
                                                         clus
vv                                                        AMP PEAK  6(4Q12) MUTATED
  CHEST - BREAST                                                                  0
  CHEST - CHEST WALL                                                              4
  CHEST - LUNG/PLEURA                                                             0
  CHEST - MEDIASTINUM                                                             0
  CHEST - OTHER (PLEASE SPECIFY                                                   0
  GYNECOLOGICAL - OVARY                                                           0
  GYNECOLOGICAL - UTERUS                                                          7
  HEAD AND NECK - HEAD                                                            2
  HEAD AND NECK - NECK                                                            0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                           0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                 2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                         0
  LOWER EXTREMITY - FOOT/ANKLE                                                    0
  LOWER EXTREMITY - GROIN                                                         1
  LOWER EXTREMITY - LOWER LEG/CALF                                                6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                         4
  LOWER EXTREMITY - THIGH/KNEE                                                   20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                       1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                         0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                      0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                              16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                              0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                              2
  SUPERFICIAL TRUNK - BACK                                                        0
  SUPERFICIAL TRUNK - BUTTOCK                                                     2
  SUPERFICIAL TRUNK - FLANK                                                       0
  UPPER EXTREMITY - SHOULDER/AXILLA                                               5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                               2
                                                         clus
vv                                                        AMP PEAK  6(4Q12) WILD-TYPE
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               2
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           21
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           2
  LOWER EXTREMITY - FOOT/ANKLE                                                      4
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           1
  LOWER EXTREMITY - THIGH/KNEE                                                     24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          5
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                             cls
clus                           0  1
  AMP PEAK  6(4Q12) MUTATED   40 38
  AMP PEAK  6(4Q12) WILD-TYPE 99 80
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED     40   38
  AMP PEAK  6(4Q12) WILD-TYPE   99   80
        clus
vv       AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  FEMALE                        40                          99
  MALE                          38                          80
[1] 2 2
[1] FALSE
D6V5, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED    46  31
  AMP PEAK  6(4Q12) WILD-TYPE 133  41
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED     46   31
  AMP PEAK  6(4Q12) WILD-TYPE  133   41
     clus
vv    AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  NO                         46                         133
  YES                        31                          41
[1] 2 2
[1] FALSE
                             vv
clus                          DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  6(4Q12) MUTATED                             11             0
  AMP PEAK  6(4Q12) WILD-TYPE                           48             2
                             vv
clus                          GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  6(4Q12) MUTATED                                                                          0
  AMP PEAK  6(4Q12) WILD-TYPE                                                                        1
                             vv
clus                          LEIOMYOSARCOMA (LMS)
  AMP PEAK  6(4Q12) MUTATED                     23
  AMP PEAK  6(4Q12) WILD-TYPE                   80
                             vv
clus                          MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  6(4Q12) MUTATED                                                  3
  AMP PEAK  6(4Q12) WILD-TYPE                                                6
                             vv
clus                          MYXOFIBROSARCOMA
  AMP PEAK  6(4Q12) MUTATED                 12
  AMP PEAK  6(4Q12) WILD-TYPE               12
                             vv
clus                          PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  6(4Q12) MUTATED                                                         15
  AMP PEAK  6(4Q12) WILD-TYPE                                                       13
                             vv
clus                          SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  6(4Q12) MUTATED                                          1
  AMP PEAK  6(4Q12) WILD-TYPE                                        1
                             vv
clus                          SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  6(4Q12) MUTATED                             0
  AMP PEAK  6(4Q12) WILD-TYPE                           2
                             vv
clus                          SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  6(4Q12) MUTATED                               0
  AMP PEAK  6(4Q12) WILD-TYPE                             6
                             vv
clus                          UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  6(4Q12) MUTATED                                           13
  AMP PEAK  6(4Q12) WILD-TYPE                                          8
D6V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  6(4Q12) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                    11
  DESMOID TUMOR                                                                                    0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                         0
  LEIOMYOSARCOMA (LMS)                                                                            23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                 3
  MYXOFIBROSARCOMA                                                                                12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                        15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                         1
  SYNOVIAL SARCOMA - BIPHASIC                                                                      0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                    0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                      13
                                                                          clus
vv                                                                         AMP PEAK  6(4Q12) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                      48
  DESMOID TUMOR                                                                                      2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           1
  LEIOMYOSARCOMA (LMS)                                                                              80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   6
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  6(4Q12) MUTATED    46  20   1  10
  AMP PEAK  6(4Q12) WILD-TYPE 106  49   8  16
D6V7, multiclass
    clus
vv   AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  R0                        46                         106
  R1                        20                          49
  R2                         1                           8
  RX                        10                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4Q12) MUTATED       3                         5    68
  AMP PEAK  6(4Q12) WILD-TYPE     3                        13   156
D6V8, multiclass
                           clus
vv                          AMP PEAK  6(4Q12) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            68
                           clus
vv                          AMP PEAK  6(4Q12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          13
  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"
D6V9, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     1  68
  AMP PEAK  6(4Q12) WILD-TYPE   4 152
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      1   68
  AMP PEAK  6(4Q12) WILD-TYPE    4  152
                        clus
vv                       AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        68                         152
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P15.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  7(5P15.33) MUTATED   67 52
  AMP PEAK  7(5P15.33) WILD-TYPE 92 46
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           119                            138 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            52                             46 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       31.53        34.68        16.18        34.36        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB3A 
       14.43        14.07        12.07       106.45        30.51        32.15 
TCGA-HB-A43Z TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       37.02        52.27        28.21        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HQ 
       20.94       188.15        35.08        50.01        19.69        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-3B-A9I3 
       88.57        44.91        54.74        10.32        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        32.71        68.61        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 
       54.21        85.02        33.53         6.28         8.58         9.70 
TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD 
        9.04        33.44        51.02         4.54        14.99        50.43 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA 
       85.45        24.26        46.03        26.47        15.95        82.68 
TCGA-DX-A6BG TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF 
       36.85        41.00        78.28        16.87        86.30        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BO 
       34.49        30.35        61.97        45.14        38.17        40.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       27.95        40.44        36.69        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A2QS 
       17.79        12.00        15.72        66.74       106.55        49.15 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       20.32        67.63         0.72        19.53         3.22        19.89 
TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-KD-A5QS 
       25.22         5.92         1.05       101.26        62.17        63.81 
TCGA-LI-A67I TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V9 
       30.31        14.99        10.45         7.36        13.08        46.82 
TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       18.08       111.98        10.52        16.77        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D 
       22.82        25.35        32.75        13.22        13.41        12.46 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC 
       84.79        38.27         8.58        63.35        26.43        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       35.18        20.65        27.32        15.95        15.98 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6YT TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X 
       36.30        67.20        17.95        15.85        40.60        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A5W3 
       22.85       101.98        60.00        84.66        16.60        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 
       52.11        26.93       159.29        22.62        11.70         8.28 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HU TCGA-3B-A9HV 
       17.52        26.17        41.49        53.49        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KY TCGA-DX-A1L4 TCGA-DX-A23R 
       42.84        38.47        36.03        12.85        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 
        5.26        76.41        66.87        27.81        60.30        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
       79.17        49.05        86.83       136.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
       35.77        10.68        73.87        68.55        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       45.99        35.28        52.77       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ 
       37.41        36.33        28.96        31.96        26.99         3.06 
TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ 
       50.50        64.21       101.23        62.20       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BZ 
       48.20        20.05         9.34        47.87       150.35         6.58 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B 
       65.98        86.10         9.21        77.88        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK 
       34.88         4.57        33.30         9.80        80.48         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
       37.12       171.09        13.58        85.97        16.41         3.91 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT 
       53.33       123.78        17.36        23.38         5.19        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       35.28        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57       122.96        37.55        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       17.65         1.84        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XO 
       64.77         0.72         8.61        19.63        10.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
        4.80        65.46        22.62        35.90        18.08        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        50.86        29.46        36.43         4.37        13.38 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        188.15                         171.09 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                         27.32                          35.08 
[1] "0.6 - 188.2 (27.3)" "0.5 - 171.1 (35.1)"
[1] "hr=" "1.5"
D7V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  7(5P15.33) MUTATED                0                  3
  AMP PEAK  7(5P15.33) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  7(5P15.33) MUTATED                     0                   0
  AMP PEAK  7(5P15.33) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                               1
  AMP PEAK  7(5P15.33) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  7(5P15.33) MUTATED                       0                     10
  AMP PEAK  7(5P15.33) WILD-TYPE                     1                     18
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  7(5P15.33) MUTATED                      2                    0
  AMP PEAK  7(5P15.33) WILD-TYPE                    0                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                                       1
  AMP PEAK  7(5P15.33) WILD-TYPE                                     1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  7(5P15.33) MUTATED                                  0
  AMP PEAK  7(5P15.33) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                                                2
  AMP PEAK  7(5P15.33) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  7(5P15.33) MUTATED                                 3
  AMP PEAK  7(5P15.33) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  7(5P15.33) MUTATED                                         1
  AMP PEAK  7(5P15.33) WILD-TYPE                                       1
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  7(5P15.33) MUTATED                              0
  AMP PEAK  7(5P15.33) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK  7(5P15.33) MUTATED                         0
  AMP PEAK  7(5P15.33) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  7(5P15.33) MUTATED                                  8
  AMP PEAK  7(5P15.33) WILD-TYPE                                9
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                                         3
  AMP PEAK  7(5P15.33) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  7(5P15.33) MUTATED                             22
  AMP PEAK  7(5P15.33) WILD-TYPE                           22
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  7(5P15.33) MUTATED                                         0
  AMP PEAK  7(5P15.33) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  7(5P15.33) MUTATED                                           1
  AMP PEAK  7(5P15.33) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  7(5P15.33) MUTATED                                                  2
  AMP PEAK  7(5P15.33) WILD-TYPE                                                3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  7(5P15.33) MUTATED                                          2
  AMP PEAK  7(5P15.33) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  7(5P15.33) MUTATED                                                         2
  AMP PEAK  7(5P15.33) WILD-TYPE                                                       0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  7(5P15.33) MUTATED                                            1
  AMP PEAK  7(5P15.33) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  7(5P15.33) MUTATED                                                  38
  AMP PEAK  7(5P15.33) WILD-TYPE                                                35
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  7(5P15.33) MUTATED                                                    0
  AMP PEAK  7(5P15.33) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  7(5P15.33) MUTATED                                    2
  AMP PEAK  7(5P15.33) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK  7(5P15.33) MUTATED                          2
  AMP PEAK  7(5P15.33) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  7(5P15.33) MUTATED                             2
  AMP PEAK  7(5P15.33) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK  7(5P15.33) MUTATED                           0
  AMP PEAK  7(5P15.33) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  7(5P15.33) MUTATED                                   7
  AMP PEAK  7(5P15.33) WILD-TYPE                                 0
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  7(5P15.33) MUTATED                                   3
  AMP PEAK  7(5P15.33) WILD-TYPE                                 2
D7V3, multiclass
                                                         clus
vv                                                        AMP PEAK  7(5P15.33) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                            10
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            1
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 38
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        AMP PEAK  7(5P15.33) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              18
  HEAD AND NECK - HEAD                                                                 0
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              1
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   35
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   59 60
  AMP PEAK  7(5P15.33) WILD-TYPE 80 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     59   60
  AMP PEAK  7(5P15.33) WILD-TYPE   80   58
        clus
vv       AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  FEMALE                           59                             80
  MALE                             60                             58
[1] 2 2
[1] FALSE
D7V5, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED    77  40
  AMP PEAK  7(5P15.33) WILD-TYPE 102  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     77   40
  AMP PEAK  7(5P15.33) WILD-TYPE  102   32
     clus
vv    AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  NO                            77                            102
  YES                           40                             32
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  7(5P15.33) MUTATED                             28             0
  AMP PEAK  7(5P15.33) WILD-TYPE                           31             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  7(5P15.33) MUTATED                                                                          0
  AMP PEAK  7(5P15.33) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK  7(5P15.33) MUTATED                     42
  AMP PEAK  7(5P15.33) WILD-TYPE                   61
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  7(5P15.33) MUTATED                                                  6
  AMP PEAK  7(5P15.33) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK  7(5P15.33) MUTATED                 11
  AMP PEAK  7(5P15.33) WILD-TYPE               13
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  7(5P15.33) MUTATED                                                         20
  AMP PEAK  7(5P15.33) WILD-TYPE                                                        8
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  7(5P15.33) MUTATED                                          1
  AMP PEAK  7(5P15.33) WILD-TYPE                                        1
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  7(5P15.33) MUTATED                             0
  AMP PEAK  7(5P15.33) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  7(5P15.33) MUTATED                               0
  AMP PEAK  7(5P15.33) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  7(5P15.33) MUTATED                                           11
  AMP PEAK  7(5P15.33) WILD-TYPE                                         10
D7V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  7(5P15.33) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       28
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               42
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            1
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         11
                                                                          clus
vv                                                                         AMP PEAK  7(5P15.33) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         31
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 61
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                     13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              1
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           10
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  7(5P15.33) MUTATED   67 32  6 13
  AMP PEAK  7(5P15.33) WILD-TYPE 85 37  3 13
D7V7, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  R0                           67                             85
  R1                           32                             37
  R2                            6                              3
  RX                           13                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P15.33) MUTATED       3                         9   103
  AMP PEAK  7(5P15.33) WILD-TYPE     3                         9   121
D7V8, multiclass
                           clus
vv                          AMP PEAK  7(5P15.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              103
                           clus
vv                          AMP PEAK  7(5P15.33) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     2 103
  AMP PEAK  7(5P15.33) WILD-TYPE   3 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      2  103
  AMP PEAK  7(5P15.33) WILD-TYPE    3  117
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            117
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P21.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P21.1) MUTATED    28  32
  AMP PEAK  8(6P21.1) WILD-TYPE 131  66
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           60                           197 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           32                            66 
$`AMP PEAK  8(6P21.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A7ET TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-KF-A41W TCGA-PC-A5DM 
       34.68        15.22        30.51        52.11        11.70         6.35 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3R-A8YX 
       35.08        50.01        19.69        88.57        44.91         0.56 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3U9 
       32.71        68.61        85.02         6.28        86.83        14.99 
TCGA-DX-A6B8 TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A8BL 
       15.95        26.99        50.50        86.30        21.30        45.14 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       38.17        27.95        36.69        60.66        19.43         1.15 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 
       66.74        77.88        49.15        67.63         4.57         0.72 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22        19.89       171.09        13.58         5.92         1.05 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A8JK TCGA-N1-A6IA 
       17.36        23.38        35.28        30.31        21.73         7.36 
TCGA-PC-A5DN TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       38.63        46.82        35.90        18.94         3.88        22.82 
TCGA-SI-AA8B TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A8C2 TCGA-X9-A971 
        8.61        12.46        22.62         8.58        35.18        27.32 

$`AMP PEAK  8(6P21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        22.85       101.98        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        37.02        12.62        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
       28.21       159.29        22.62        17.75         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP 
       20.94       188.15        17.52        26.17        41.49        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       68.55        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY 
       38.47        36.03        18.64        26.56        14.04        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        18.54        54.21        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
        9.70        95.38        79.17         9.04        49.05       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YR 
       36.33        28.96        31.96        36.85         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM 
       78.28        16.87        64.21       101.23        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ 
       61.97        47.87        40.77       150.35        40.44         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S 
       17.79        12.00        15.72        65.98        86.10         9.21 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
      106.55        50.40        50.89        71.31        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 
       20.32        19.89        15.48         8.05        34.88        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48        19.53         1.38        37.12        25.22 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       85.97        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA 
      123.78         5.19        63.81        16.41        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        37.55        81.01        13.08        17.65         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       10.52         0.72        16.77        25.35        32.75        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22        13.41        10.72        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        63.35        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        19.17        20.65        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                       171.09                        188.15 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                       27.155                        32.150 
[1] "0.6 - 171.1 (27.2)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.9"
D8V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  8(6P21.1) MUTATED                0                  1
  AMP PEAK  8(6P21.1) WILD-TYPE              1                  6
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  8(6P21.1) MUTATED                     0                   0
  AMP PEAK  8(6P21.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  8(6P21.1) MUTATED                               0
  AMP PEAK  8(6P21.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  8(6P21.1) MUTATED                       0                      9
  AMP PEAK  8(6P21.1) WILD-TYPE                     1                     19
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  8(6P21.1) MUTATED                      0                    0
  AMP PEAK  8(6P21.1) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  8(6P21.1) MUTATED                                       0
  AMP PEAK  8(6P21.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  8(6P21.1) MUTATED                                  0
  AMP PEAK  8(6P21.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  8(6P21.1) MUTATED                                                1
  AMP PEAK  8(6P21.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  8(6P21.1) MUTATED                                 3
  AMP PEAK  8(6P21.1) WILD-TYPE                               7
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  8(6P21.1) MUTATED                                         0
  AMP PEAK  8(6P21.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  8(6P21.1) MUTATED                              0
  AMP PEAK  8(6P21.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  8(6P21.1) MUTATED                         0
  AMP PEAK  8(6P21.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  8(6P21.1) MUTATED                                  2
  AMP PEAK  8(6P21.1) WILD-TYPE                               15
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  8(6P21.1) MUTATED                                         2
  AMP PEAK  8(6P21.1) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  8(6P21.1) MUTATED                             18
  AMP PEAK  8(6P21.1) WILD-TYPE                           26
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  8(6P21.1) MUTATED                                         0
  AMP PEAK  8(6P21.1) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  8(6P21.1) MUTATED                                           0
  AMP PEAK  8(6P21.1) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  8(6P21.1) MUTATED                                                  0
  AMP PEAK  8(6P21.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  8(6P21.1) MUTATED                                          2
  AMP PEAK  8(6P21.1) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  8(6P21.1) MUTATED                                                         1
  AMP PEAK  8(6P21.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  8(6P21.1) MUTATED                                            0
  AMP PEAK  8(6P21.1) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  8(6P21.1) MUTATED                                                  14
  AMP PEAK  8(6P21.1) WILD-TYPE                                                59
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  8(6P21.1) MUTATED                                                    0
  AMP PEAK  8(6P21.1) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  8(6P21.1) MUTATED                                    1
  AMP PEAK  8(6P21.1) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  8(6P21.1) MUTATED                          0
  AMP PEAK  8(6P21.1) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  8(6P21.1) MUTATED                             1
  AMP PEAK  8(6P21.1) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  8(6P21.1) MUTATED                           0
  AMP PEAK  8(6P21.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  8(6P21.1) MUTATED                                   3
  AMP PEAK  8(6P21.1) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  8(6P21.1) MUTATED                                   2
  AMP PEAK  8(6P21.1) WILD-TYPE                                 3
D8V3, multiclass
                                                         clus
vv                                                        AMP PEAK  8(6P21.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                1
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            9
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        AMP PEAK  8(6P21.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  6
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             19
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED    29  31
  AMP PEAK  8(6P21.1) WILD-TYPE 110  87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED     29   31
  AMP PEAK  8(6P21.1) WILD-TYPE  110   87
        clus
vv       AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  FEMALE                          29                           110
  MALE                            31                            87
[1] 2 2
[1] FALSE
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED    35  24
  AMP PEAK  8(6P21.1) WILD-TYPE 144  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED     35   24
  AMP PEAK  8(6P21.1) WILD-TYPE  144   48
     clus
vv    AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  NO                           35                           144
  YES                          24                            48
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  8(6P21.1) MUTATED                             13             0
  AMP PEAK  8(6P21.1) WILD-TYPE                           46             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  8(6P21.1) MUTATED                                                                          0
  AMP PEAK  8(6P21.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  8(6P21.1) MUTATED                     19
  AMP PEAK  8(6P21.1) WILD-TYPE                   84
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  8(6P21.1) MUTATED                                                  1
  AMP PEAK  8(6P21.1) WILD-TYPE                                                8
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  8(6P21.1) MUTATED                  7
  AMP PEAK  8(6P21.1) WILD-TYPE               17
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  8(6P21.1) MUTATED                                                         11
  AMP PEAK  8(6P21.1) WILD-TYPE                                                       17
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  8(6P21.1) MUTATED                                          0
  AMP PEAK  8(6P21.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  8(6P21.1) MUTATED                             0
  AMP PEAK  8(6P21.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  8(6P21.1) MUTATED                               0
  AMP PEAK  8(6P21.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  8(6P21.1) MUTATED                                            9
  AMP PEAK  8(6P21.1) WILD-TYPE                                         12
D8V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  8(6P21.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      13
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              19
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   1
  MYXOFIBROSARCOMA                                                                                   7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         9
                                                                          clus
vv                                                                         AMP PEAK  8(6P21.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        46
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                84
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     8
  MYXOFIBROSARCOMA                                                                                    17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P21.1) MUTATED    30  20   3   7
  AMP PEAK  8(6P21.1) WILD-TYPE 122  49   6  19
D8V7, multiclass
    clus
vv   AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  R0                          30                           122
  R1                          20                            49
  R2                           3                             6
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P21.1) MUTATED       0                         7    50
  AMP PEAK  8(6P21.1) WILD-TYPE     6                        11   174
D8V8, multiclass
                           clus
vv                          AMP PEAK  8(6P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              50
                           clus
vv                          AMP PEAK  8(6P21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            11
  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"
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED     2  51
  AMP PEAK  8(6P21.1) WILD-TYPE   3 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED      2   51
  AMP PEAK  8(6P21.1) WILD-TYPE    3  169
                        clus
vv                       AMP PEAK  8(6P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       AMP PEAK  8(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           169
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q25.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(6Q25.1) MUTATED    47  28
  AMP PEAK  9(6Q25.1) WILD-TYPE 112  70
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           75                           182 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           28                            70 
$`AMP PEAK  9(6Q25.1) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HB-A43Z 
       16.18        34.36        15.22        30.51        16.60        37.02 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-X6-A8C6 TCGA-3B-A9HI 
       17.75         8.28         6.35        20.94        35.08        50.01 
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L4 
       44.91         0.56        32.71        68.61        45.11        66.94 
TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
        5.26        27.81        95.38        49.05        86.83        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A48N TCGA-DX-A6B8 
       44.68        31.86        35.77        14.99        35.28        15.95 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A7ES 
       26.99        41.00        78.28        50.50        64.21        20.05 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU 
       61.97        45.14        47.87        40.77        27.95        36.69 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2S 
       19.43         1.15        12.00        15.72        86.10         9.21 
TCGA-DX-AB2T TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
       77.88        67.63         3.22        19.89        37.12       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QU TCGA-LI-A67I 
        5.92         1.05        17.36        23.38        35.28        30.31 
TCGA-MB-A8JK TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-SG-A6Z4 
       21.73        37.55        13.08        48.59        35.90        18.94 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB 
       25.35        32.75        13.41        84.79        38.27         8.58 
TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X9-A971 
       26.43        19.17        27.32 

$`AMP PEAK  9(6Q25.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        34.68        67.20        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85       101.98        60.00        84.66        32.15 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       12.62        52.11        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
       22.62        11.70        18.08       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       41.49        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       18.64        26.56        14.04        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       85.02        33.53        74.66        76.41        66.87         6.28 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW 
       60.30         8.58         9.70        79.17         9.04       136.44 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        10.68        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       34.88        85.45         9.73        45.99        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6YQ 
       82.68        36.33        28.96        31.96        36.85         3.06 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       16.87        86.30       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BJ TCGA-DX-A8BN 
       30.35       152.12        29.49        48.20         9.34        38.17 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2L 
      150.35        40.44        60.66         6.58        17.79        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       66.74       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.53         1.38        25.22        13.58        85.97        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV 
        3.91       101.26        53.33        62.17       123.78         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       63.81        16.41        25.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       16.77         3.88        22.82         8.61        19.63        13.22 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 
       10.72        12.46        11.93         4.80        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        35.90        18.08        45.34        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                       171.09                        188.15 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                       31.860                        30.985 
[1] "0.6 - 171.1 (31.9)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.1"
D9V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK  9(6Q25.1) MUTATED                0                  3
  AMP PEAK  9(6Q25.1) WILD-TYPE              1                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK  9(6Q25.1) MUTATED                     0                   0
  AMP PEAK  9(6Q25.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK  9(6Q25.1) MUTATED                               0
  AMP PEAK  9(6Q25.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK  9(6Q25.1) MUTATED                       0                      5
  AMP PEAK  9(6Q25.1) WILD-TYPE                     1                     23
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK  9(6Q25.1) MUTATED                      1                    0
  AMP PEAK  9(6Q25.1) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK  9(6Q25.1) MUTATED                                       0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK  9(6Q25.1) MUTATED                                  0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK  9(6Q25.1) MUTATED                                                1
  AMP PEAK  9(6Q25.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK  9(6Q25.1) MUTATED                                 3
  AMP PEAK  9(6Q25.1) WILD-TYPE                               7
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK  9(6Q25.1) MUTATED                                         0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK  9(6Q25.1) MUTATED                              0
  AMP PEAK  9(6Q25.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK  9(6Q25.1) MUTATED                         1
  AMP PEAK  9(6Q25.1) WILD-TYPE                       1
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK  9(6Q25.1) MUTATED                                  5
  AMP PEAK  9(6Q25.1) WILD-TYPE                               12
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK  9(6Q25.1) MUTATED                                         2
  AMP PEAK  9(6Q25.1) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK  9(6Q25.1) MUTATED                             17
  AMP PEAK  9(6Q25.1) WILD-TYPE                           27
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK  9(6Q25.1) MUTATED                                         0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK  9(6Q25.1) MUTATED                                           2
  AMP PEAK  9(6Q25.1) WILD-TYPE                                         0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK  9(6Q25.1) MUTATED                                                  0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK  9(6Q25.1) MUTATED                                          0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                        8
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK  9(6Q25.1) MUTATED                                                         0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK  9(6Q25.1) MUTATED                                            0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK  9(6Q25.1) MUTATED                                                  24
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                49
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK  9(6Q25.1) MUTATED                                                    0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK  9(6Q25.1) MUTATED                                    1
  AMP PEAK  9(6Q25.1) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK  9(6Q25.1) MUTATED                          2
  AMP PEAK  9(6Q25.1) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK  9(6Q25.1) MUTATED                             1
  AMP PEAK  9(6Q25.1) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK  9(6Q25.1) MUTATED                           0
  AMP PEAK  9(6Q25.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK  9(6Q25.1) MUTATED                                   4
  AMP PEAK  9(6Q25.1) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK  9(6Q25.1) MUTATED                                   2
  AMP PEAK  9(6Q25.1) WILD-TYPE                                 3
D9V3, multiclass
                                                         clus
vv                                                        AMP PEAK  9(6Q25.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            5
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                24
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        AMP PEAK  9(6Q25.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             23
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  49
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                               cls
clus                              0   1
  AMP PEAK  9(6Q25.1) MUTATED    34  41
  AMP PEAK  9(6Q25.1) WILD-TYPE 105  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6Q25.1) MUTATED     34   41
  AMP PEAK  9(6Q25.1) WILD-TYPE  105   77
        clus
vv       AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE
  FEMALE                          34                           105
  MALE                            41                            77
[1] 2 2
[1] FALSE
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(6Q25.1) MUTATED    47  27
  AMP PEAK  9(6Q25.1) WILD-TYPE 132  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6Q25.1) MUTATED     47   27
  AMP PEAK  9(6Q25.1) WILD-TYPE  132   45
     clus
vv    AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE
  NO                           47                           132
  YES                          27                            45
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK  9(6Q25.1) MUTATED                             24             0
  AMP PEAK  9(6Q25.1) WILD-TYPE                           35             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK  9(6Q25.1) MUTATED                                                                          0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK  9(6Q25.1) MUTATED                     17
  AMP PEAK  9(6Q25.1) WILD-TYPE                   86
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK  9(6Q25.1) MUTATED                                                  2
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK  9(6Q25.1) MUTATED                 12
  AMP PEAK  9(6Q25.1) WILD-TYPE               12
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK  9(6Q25.1) MUTATED                                                         15
  AMP PEAK  9(6Q25.1) WILD-TYPE                                                       13
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK  9(6Q25.1) MUTATED                                          0
  AMP PEAK  9(6Q25.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK  9(6Q25.1) MUTATED                             0
  AMP PEAK  9(6Q25.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK  9(6Q25.1) MUTATED                               0
  AMP PEAK  9(6Q25.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK  9(6Q25.1) MUTATED                                            5
  AMP PEAK  9(6Q25.1) WILD-TYPE                                         16
D9V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK  9(6Q25.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      24
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         5
                                                                          clus
vv                                                                         AMP PEAK  9(6Q25.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        35
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(6Q25.1) MUTATED    40  25   4   6
  AMP PEAK  9(6Q25.1) WILD-TYPE 112  44   5  20
D9V7, multiclass
    clus
vv   AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE
  R0                          40                           112
  R1                          25                            44
  R2                           4                             5
  RX                           6                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q25.1) MUTATED       2                         6    66
  AMP PEAK  9(6Q25.1) WILD-TYPE     4                        12   158
D9V8, multiclass
                           clus
vv                          AMP PEAK  9(6Q25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              66
                           clus
vv                          AMP PEAK  9(6Q25.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                               cls
clus                              0   1
  AMP PEAK  9(6Q25.1) MUTATED     2  64
  AMP PEAK  9(6Q25.1) WILD-TYPE   3 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6Q25.1) MUTATED      2   64
  AMP PEAK  9(6Q25.1) WILD-TYPE    3  156
                        clus
vv                       AMP PEAK  9(6Q25.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       AMP PEAK  9(6Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q31.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7Q31.2) MUTATED    42  35
  AMP PEAK 10(7Q31.2) WILD-TYPE 117  63
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           77                           180 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           35                            63 
$`AMP PEAK 10(7Q31.2) MUTATED`
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB37 
       14.43        15.85       106.45        13.28        30.51        84.66 
TCGA-HB-A43Z TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
       37.02         8.28        20.94       188.15        17.52        26.17 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3B-A9HX TCGA-DX-A1KX TCGA-DX-A1KY 
       35.08        50.01        44.91        42.84        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A3LT 
       45.11        54.21        85.02         6.28        27.81        49.05 
TCGA-DX-A3M1 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BH 
       44.68        85.45        24.26        15.95        36.33        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        41.00        50.50        16.87        86.30        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR 
       21.30        34.49        62.20        61.97        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2S TCGA-DX-AB2V TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
       12.00         9.21       106.55        21.70        67.63         4.57 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VF 
        0.72        19.53         3.22        19.89        13.58         1.05 
TCGA-K1-A6RU TCGA-KD-A5QU TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QC-AA9N 
       23.38        35.28        10.45        37.55        13.08        17.65 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SI-A71O TCGA-UE-A6QU 
       18.08        35.90       111.98        16.77        22.82        13.41 
TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X9-A973 
       11.93        22.62        45.34        35.18        36.43 

$`AMP PEAK 10(7Q31.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        15.22        17.95        14.07        40.60        12.07 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 
       22.85       101.98        60.00        32.15        16.60        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT TCGA-3B-A9HL 
       11.70        17.75         6.35        18.08        41.49        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        54.74        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       14.04        32.71        18.54        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        66.87        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        50.43        34.88         9.73        45.99 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.58        37.41        82.68        28.96        31.96        36.85 
TCGA-DX-A6YS TCGA-DX-A6Z2 TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       78.28       101.23        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BV 
       20.05         9.34        45.14        47.87        38.17        60.66 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T 
       17.79        15.72        65.98        86.10        66.74        77.88 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO 
       50.40        50.89        71.31        49.15        31.13        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA 
       19.89        15.48         8.05        34.88        33.30         9.80 
TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 
       80.48         1.38        37.12        25.22       171.09        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
      123.78        17.36         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
        1.84        46.82        48.59        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        18.94         3.88        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XQ 
        8.61        19.63        13.22        10.72        12.46         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        65.46         8.58        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       35.90        18.08        30.84        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        27.32         4.37        13.38        15.95        15.98 

  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                         0.72                          0.49 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                       188.15                        171.09 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                        27.81                         31.91 
[1] "0.7 - 188.2 (27.8)" "0.5 - 171.1 (31.9)"
[1] "hr=" "1.4"
D10V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 10(7Q31.2) MUTATED                0                  2
  AMP PEAK 10(7Q31.2) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 10(7Q31.2) MUTATED                     0                   0
  AMP PEAK 10(7Q31.2) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 10(7Q31.2) MUTATED                               0
  AMP PEAK 10(7Q31.2) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 10(7Q31.2) MUTATED                       1                      4
  AMP PEAK 10(7Q31.2) WILD-TYPE                     0                     24
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 10(7Q31.2) MUTATED                      1                    0
  AMP PEAK 10(7Q31.2) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 10(7Q31.2) MUTATED                                       0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 10(7Q31.2) MUTATED                                  0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 10(7Q31.2) MUTATED                                                0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 10(7Q31.2) MUTATED                                 5
  AMP PEAK 10(7Q31.2) WILD-TYPE                               5
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 10(7Q31.2) MUTATED                                         0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 10(7Q31.2) MUTATED                              0
  AMP PEAK 10(7Q31.2) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK 10(7Q31.2) MUTATED                         0
  AMP PEAK 10(7Q31.2) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 10(7Q31.2) MUTATED                                  7
  AMP PEAK 10(7Q31.2) WILD-TYPE                               10
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 10(7Q31.2) MUTATED                                         2
  AMP PEAK 10(7Q31.2) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 10(7Q31.2) MUTATED                             18
  AMP PEAK 10(7Q31.2) WILD-TYPE                           26
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 10(7Q31.2) MUTATED                                         1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 10(7Q31.2) MUTATED                                           0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 10(7Q31.2) MUTATED                                                  1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 10(7Q31.2) MUTATED                                          1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                        7
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 10(7Q31.2) MUTATED                                                         0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 10(7Q31.2) MUTATED                                            0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 10(7Q31.2) MUTATED                                                  19
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                54
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 10(7Q31.2) MUTATED                                                    0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 10(7Q31.2) MUTATED                                    1
  AMP PEAK 10(7Q31.2) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK 10(7Q31.2) MUTATED                          3
  AMP PEAK 10(7Q31.2) WILD-TYPE                        2
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 10(7Q31.2) MUTATED                             4
  AMP PEAK 10(7Q31.2) WILD-TYPE                           0
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK 10(7Q31.2) MUTATED                           0
  AMP PEAK 10(7Q31.2) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 10(7Q31.2) MUTATED                                   4
  AMP PEAK 10(7Q31.2) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 10(7Q31.2) MUTATED                                   3
  AMP PEAK 10(7Q31.2) WILD-TYPE                                 2
D10V3, multiclass
                                                         clus
vv                                                        AMP PEAK 10(7Q31.2) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                            4
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                19
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          3
  SUPERFICIAL TRUNK - BUTTOCK                                                       4
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        AMP PEAK 10(7Q31.2) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                             24
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  54
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            2
  SUPERFICIAL TRUNK - BUTTOCK                                                         0
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                               cls
clus                             0  1
  AMP PEAK 10(7Q31.2) MUTATED   41 36
  AMP PEAK 10(7Q31.2) WILD-TYPE 98 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED     41   36
  AMP PEAK 10(7Q31.2) WILD-TYPE   98   82
        clus
vv       AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  FEMALE                          41                            98
  MALE                            36                            82
[1] 2 2
[1] FALSE
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED    46  30
  AMP PEAK 10(7Q31.2) WILD-TYPE 133  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED     46   30
  AMP PEAK 10(7Q31.2) WILD-TYPE  133   42
     clus
vv    AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  NO                           46                           133
  YES                          30                            42
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 10(7Q31.2) MUTATED                             18             0
  AMP PEAK 10(7Q31.2) WILD-TYPE                           41             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 10(7Q31.2) MUTATED                                                                          0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK 10(7Q31.2) MUTATED                     20
  AMP PEAK 10(7Q31.2) WILD-TYPE                   83
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 10(7Q31.2) MUTATED                                                  3
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                6
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK 10(7Q31.2) MUTATED                 10
  AMP PEAK 10(7Q31.2) WILD-TYPE               14
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 10(7Q31.2) MUTATED                                                         14
  AMP PEAK 10(7Q31.2) WILD-TYPE                                                       14
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 10(7Q31.2) MUTATED                                          0
  AMP PEAK 10(7Q31.2) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 10(7Q31.2) MUTATED                             0
  AMP PEAK 10(7Q31.2) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 10(7Q31.2) MUTATED                               0
  AMP PEAK 10(7Q31.2) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 10(7Q31.2) MUTATED                                           12
  AMP PEAK 10(7Q31.2) WILD-TYPE                                          9
D10V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 10(7Q31.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      18
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   3
  MYXOFIBROSARCOMA                                                                                  10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        12
                                                                          clus
vv                                                                         AMP PEAK 10(7Q31.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        41
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     6
  MYXOFIBROSARCOMA                                                                                    14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7Q31.2) MUTATED    44  21   3   8
  AMP PEAK 10(7Q31.2) WILD-TYPE 108  48   6  18
D10V7, multiclass
    clus
vv   AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  R0                          44                           108
  R1                          21                            48
  R2                           3                             6
  RX                           8                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q31.2) MUTATED       2                         5    67
  AMP PEAK 10(7Q31.2) WILD-TYPE     4                        13   157
D10V8, multiclass
                           clus
vv                          AMP PEAK 10(7Q31.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              67
                           clus
vv                          AMP PEAK 10(7Q31.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            13
  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"
D10V9, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED     2  68
  AMP PEAK 10(7Q31.2) WILD-TYPE   3 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED      2   68
  AMP PEAK 10(7Q31.2) WILD-TYPE    3  152
                        clus
vv                       AMP PEAK 10(7Q31.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       AMP PEAK 10(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           152
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8P11.22) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8P11.22) MUTATED    41  40
  AMP PEAK 11(8P11.22) WILD-TYPE 118  58
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            81                            176 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            40                             58 
$`AMP PEAK 11(8P11.22) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       34.68        34.36        14.43        12.07       106.45        22.85 
TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-KF-A41W TCGA-PC-A5DM TCGA-SG-A849 
       30.51        52.11        52.27        11.70         6.35        17.52 
TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HT TCGA-3B-A9I1 
       26.17        35.08        50.01        19.69        54.74        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ 
       26.56         0.56        14.04        32.71        12.85        45.11 
TCGA-DX-A23R TCGA-DX-A3LS TCGA-DX-A3M1 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF 
       74.66         9.04        44.68         4.54        14.99        85.45 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX 
       15.95        82.68         3.06        41.00        78.28        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BK 
       86.30       101.23        21.30        62.20         9.34        61.97 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2Q 
       38.17        40.77        27.95        36.69        19.43        66.74 
TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
      106.55        31.13         4.57        80.48        19.53         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
       19.89        37.12        25.22        13.58         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MJ-A68H TCGA-MJ-A68J 
        1.05        23.38        63.81        35.28        14.99        17.98 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-RN-AAAQ 
       10.45         7.36        37.55        18.08       111.98        16.77 
TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-WP-A9GB 
       18.94         8.61        13.22        13.41        22.62         8.58 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A971 
       45.34        19.17        27.32 

$`AMP PEAK 11(8P11.22) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB32 
       17.95        14.07        15.85        40.60        13.28       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       26.93        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ 
       18.08        20.94       188.15        41.49        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        44.91        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.47        36.03        68.61        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        66.94         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        33.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       51.02        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47       108.82        59.84        37.58        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6Z0 
       28.96        31.96        36.85        26.99        50.50        64.21 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       45.14        47.87       150.35        40.44        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EK TCGA-IS-A3K7 
       34.88        33.30         0.72         9.80         1.38       171.09 
TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       85.97         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       17.36         5.19        16.41        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       21.73        19.73        22.39        11.57       122.96        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       81.01        13.08        17.65         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       35.90        37.12       130.32        64.77        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80G 
        3.88        22.82        25.35        32.75        19.63        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                        111.98                         188.15 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                         22.85                          34.01 
[1] "0.6 - 112.0 (22.9)" "0.5 - 188.2 (34.0)"
[1] "hr=" "1.8"
D11V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 11(8P11.22) MUTATED                0                  4
  AMP PEAK 11(8P11.22) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 11(8P11.22) MUTATED                     0                   0
  AMP PEAK 11(8P11.22) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 11(8P11.22) MUTATED                               0
  AMP PEAK 11(8P11.22) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 11(8P11.22) MUTATED                       0                      9
  AMP PEAK 11(8P11.22) WILD-TYPE                     1                     19
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 11(8P11.22) MUTATED                      1                    0
  AMP PEAK 11(8P11.22) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 11(8P11.22) MUTATED                                       1
  AMP PEAK 11(8P11.22) WILD-TYPE                                     1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 11(8P11.22) MUTATED                                  0
  AMP PEAK 11(8P11.22) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 11(8P11.22) MUTATED                                                2
  AMP PEAK 11(8P11.22) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 11(8P11.22) MUTATED                                 3
  AMP PEAK 11(8P11.22) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 11(8P11.22) MUTATED                                         1
  AMP PEAK 11(8P11.22) WILD-TYPE                                       1
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 11(8P11.22) MUTATED                              0
  AMP PEAK 11(8P11.22) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 11(8P11.22) MUTATED                         0
  AMP PEAK 11(8P11.22) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 11(8P11.22) MUTATED                                  7
  AMP PEAK 11(8P11.22) WILD-TYPE                               10
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 11(8P11.22) MUTATED                                         3
  AMP PEAK 11(8P11.22) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 11(8P11.22) MUTATED                             19
  AMP PEAK 11(8P11.22) WILD-TYPE                           25
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 11(8P11.22) MUTATED                                         0
  AMP PEAK 11(8P11.22) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 11(8P11.22) MUTATED                                           0
  AMP PEAK 11(8P11.22) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 11(8P11.22) MUTATED                                                  1
  AMP PEAK 11(8P11.22) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 11(8P11.22) MUTATED                                          2
  AMP PEAK 11(8P11.22) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 11(8P11.22) MUTATED                                                         0
  AMP PEAK 11(8P11.22) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 11(8P11.22) MUTATED                                            0
  AMP PEAK 11(8P11.22) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 11(8P11.22) MUTATED                                                  19
  AMP PEAK 11(8P11.22) WILD-TYPE                                                54
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 11(8P11.22) MUTATED                                                    0
  AMP PEAK 11(8P11.22) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 11(8P11.22) MUTATED                                    1
  AMP PEAK 11(8P11.22) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 11(8P11.22) MUTATED                          1
  AMP PEAK 11(8P11.22) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 11(8P11.22) MUTATED                             1
  AMP PEAK 11(8P11.22) WILD-TYPE                           3
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 11(8P11.22) MUTATED                           0
  AMP PEAK 11(8P11.22) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 11(8P11.22) MUTATED                                   4
  AMP PEAK 11(8P11.22) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 11(8P11.22) MUTATED                                   2
  AMP PEAK 11(8P11.22) WILD-TYPE                                 3
D11V3, multiclass
                                                         clus
vv                                                        AMP PEAK 11(8P11.22) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             9
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            1
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 19
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        1
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        AMP PEAK 11(8P11.22) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              19
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              1
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   54
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          3
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                                cls
clus                              0  1
  AMP PEAK 11(8P11.22) MUTATED   44 37
  AMP PEAK 11(8P11.22) WILD-TYPE 95 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.22) MUTATED     44   37
  AMP PEAK 11(8P11.22) WILD-TYPE   95   81
        clus
vv       AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE
  FEMALE                           44                             95
  MALE                             37                             81
[1] 2 2
[1] FALSE
D11V5, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.22) MUTATED    50  29
  AMP PEAK 11(8P11.22) WILD-TYPE 129  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.22) MUTATED     50   29
  AMP PEAK 11(8P11.22) WILD-TYPE  129   43
     clus
vv    AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE
  NO                            50                            129
  YES                           29                             43
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 11(8P11.22) MUTATED                             14             0
  AMP PEAK 11(8P11.22) WILD-TYPE                           45             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 11(8P11.22) MUTATED                                                                          0
  AMP PEAK 11(8P11.22) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 11(8P11.22) MUTATED                     32
  AMP PEAK 11(8P11.22) WILD-TYPE                   71
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 11(8P11.22) MUTATED                                                  1
  AMP PEAK 11(8P11.22) WILD-TYPE                                                8
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 11(8P11.22) MUTATED                 12
  AMP PEAK 11(8P11.22) WILD-TYPE               12
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 11(8P11.22) MUTATED                                                         13
  AMP PEAK 11(8P11.22) WILD-TYPE                                                       15
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 11(8P11.22) MUTATED                                          0
  AMP PEAK 11(8P11.22) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 11(8P11.22) MUTATED                             0
  AMP PEAK 11(8P11.22) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 11(8P11.22) MUTATED                               0
  AMP PEAK 11(8P11.22) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 11(8P11.22) MUTATED                                            9
  AMP PEAK 11(8P11.22) WILD-TYPE                                         12
D11V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 11(8P11.22) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       14
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    1
  MYXOFIBROSARCOMA                                                                                   12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          9
                                                                          clus
vv                                                                         AMP PEAK 11(8P11.22) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         45
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      8
  MYXOFIBROSARCOMA                                                                                     12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(8P11.22) MUTATED    44  24   4   8
  AMP PEAK 11(8P11.22) WILD-TYPE 108  45   5  18
D11V7, multiclass
    clus
vv   AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE
  R0                           44                            108
  R1                           24                             45
  R2                            4                              5
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8P11.22) MUTATED       4                         7    65
  AMP PEAK 11(8P11.22) WILD-TYPE     2                        11   159
D11V8, multiclass
                           clus
vv                          AMP PEAK 11(8P11.22) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               65
                           clus
vv                          AMP PEAK 11(8P11.22) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.22) MUTATED     2  71
  AMP PEAK 11(8P11.22) WILD-TYPE   3 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.22) MUTATED      2   71
  AMP PEAK 11(8P11.22) WILD-TYPE    3  149
                        clus
vv                       AMP PEAK 11(8P11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK 11(8P11.22) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            149
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    43  40
  AMP PEAK 12(8Q24.21) WILD-TYPE 116  58
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            83                            174 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            40                             58 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 
       34.36        14.43        14.07        12.07        13.28        22.85 
TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-LI-A9QH 
       30.51        16.60        37.02        52.11        52.27        17.75 
TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 
       17.52        26.17        53.49        54.74        42.84        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 
       26.56         0.56        14.04        12.85        45.11        85.02 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       74.66         6.28        51.02         4.54        14.99        10.68 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF 
       85.45        35.28        26.47        15.95        82.68        31.96 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BL 
       50.50        16.87       101.23        62.20         9.34        45.14 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q 
       47.87        40.77        19.43        17.79        86.10        66.74 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ 
       49.15        31.13         0.72        80.48        19.53        25.22 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU 
        5.92         1.05         3.91         5.19        63.81        35.28 
TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
       25.41        21.73        14.99        17.98        10.45         7.36 
TCGA-PC-A5DL TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 
       37.55        46.82        48.59        10.52        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        22.82        32.75         8.61        13.22        13.41 
TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-Z4-AAPG 
       10.72        22.62        26.43        19.17        15.98 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB32 
       15.22        17.95        15.85        40.60       106.45       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 
       60.00        84.66        32.15        12.62        26.93        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP 
      159.29        22.62        11.70         8.28         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94       188.15        41.49        35.08        50.01        19.69 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       68.55        88.57        44.91        25.25        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 
       38.47        36.03        32.71        68.61        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       35.77        73.87        68.55        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       45.99        24.26        52.77        46.03       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       37.58        37.41        36.33        28.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
        3.06        41.00        78.28        86.30        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       61.97        38.17       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66         6.58         1.15        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A4EK 
       34.88         4.57        33.30         9.80         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.89        37.12       171.09        13.58        85.97        16.41 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47P 
       16.41        30.31         0.49        19.73        22.39        11.57 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        35.90        37.12       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-SI-A71P TCGA-SI-AA8C TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
        0.72        25.35        19.63        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        38.27        65.46         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        30.84        35.18        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        101.23                         188.15 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         22.62                          34.88 
[1] "0.6 - 101.2 (22.6)" "0.5 - 188.2 (34.9)"
[1] "hr=" "1.9"
D12V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 12(8Q24.21) MUTATED                0                  4
  AMP PEAK 12(8Q24.21) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 12(8Q24.21) MUTATED                     0                   0
  AMP PEAK 12(8Q24.21) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                               1
  AMP PEAK 12(8Q24.21) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 12(8Q24.21) MUTATED                       0                      9
  AMP PEAK 12(8Q24.21) WILD-TYPE                     1                     19
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 12(8Q24.21) MUTATED                      1                    0
  AMP PEAK 12(8Q24.21) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                                       1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                     1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 12(8Q24.21) MUTATED                                  0
  AMP PEAK 12(8Q24.21) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                                                2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 12(8Q24.21) MUTATED                                 2
  AMP PEAK 12(8Q24.21) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 12(8Q24.21) MUTATED                                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                       1
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 12(8Q24.21) MUTATED                              1
  AMP PEAK 12(8Q24.21) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 12(8Q24.21) MUTATED                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 12(8Q24.21) MUTATED                                 10
  AMP PEAK 12(8Q24.21) WILD-TYPE                                7
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                                         2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 12(8Q24.21) MUTATED                             15
  AMP PEAK 12(8Q24.21) WILD-TYPE                           29
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 12(8Q24.21) MUTATED                                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 12(8Q24.21) MUTATED                                           1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 12(8Q24.21) MUTATED                                                  1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 12(8Q24.21) MUTATED                                          2
  AMP PEAK 12(8Q24.21) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 12(8Q24.21) MUTATED                                                         1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 12(8Q24.21) MUTATED                                            0
  AMP PEAK 12(8Q24.21) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 12(8Q24.21) MUTATED                                                  20
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                53
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 12(8Q24.21) MUTATED                                                    0
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 12(8Q24.21) MUTATED                                    1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 12(8Q24.21) MUTATED                          0
  AMP PEAK 12(8Q24.21) WILD-TYPE                        5
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 12(8Q24.21) MUTATED                             0
  AMP PEAK 12(8Q24.21) WILD-TYPE                           4
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 12(8Q24.21) MUTATED                           0
  AMP PEAK 12(8Q24.21) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 12(8Q24.21) MUTATED                                   5
  AMP PEAK 12(8Q24.21) WILD-TYPE                                 2
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 12(8Q24.21) MUTATED                                   1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                 4
D12V3, multiclass
                                                         clus
vv                                                        AMP PEAK 12(8Q24.21) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             9
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            1
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                      15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 20
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                                        0
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        AMP PEAK 12(8Q24.21) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              19
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              1
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   53
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                                          4
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   44 39
  AMP PEAK 12(8Q24.21) WILD-TYPE 95 79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     44   39
  AMP PEAK 12(8Q24.21) WILD-TYPE   95   79
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           44                             95
  MALE                             39                             79
[1] 2 2
[1] FALSE
D12V5, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    57  25
  AMP PEAK 12(8Q24.21) WILD-TYPE 122  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     57   25
  AMP PEAK 12(8Q24.21) WILD-TYPE  122   47
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            57                            122
  YES                           25                             47
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 12(8Q24.21) MUTATED                             13             0
  AMP PEAK 12(8Q24.21) WILD-TYPE                           46             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 12(8Q24.21) MUTATED                                                                          0
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 12(8Q24.21) MUTATED                     34
  AMP PEAK 12(8Q24.21) WILD-TYPE                   69
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 12(8Q24.21) MUTATED                                                  4
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                5
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 12(8Q24.21) MUTATED                  8
  AMP PEAK 12(8Q24.21) WILD-TYPE               16
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 12(8Q24.21) MUTATED                                                         14
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                       14
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 12(8Q24.21) MUTATED                                          0
  AMP PEAK 12(8Q24.21) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 12(8Q24.21) MUTATED                             0
  AMP PEAK 12(8Q24.21) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 12(8Q24.21) MUTATED                               0
  AMP PEAK 12(8Q24.21) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 12(8Q24.21) MUTATED                                           10
  AMP PEAK 12(8Q24.21) WILD-TYPE                                         11
D12V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 12(8Q24.21) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       13
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               34
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    4
  MYXOFIBROSARCOMA                                                                                    8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         10
                                                                          clus
vv                                                                         AMP PEAK 12(8Q24.21) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         46
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 69
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      5
  MYXOFIBROSARCOMA                                                                                     16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           11
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8Q24.21) MUTATED    47  21   6   8
  AMP PEAK 12(8Q24.21) WILD-TYPE 105  48   3  18
D12V7, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  R0                           47                            105
  R1                           21                             48
  R2                            6                              3
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       4                         6    68
  AMP PEAK 12(8Q24.21) WILD-TYPE     2                        12   156
D12V8, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               68
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             12
  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"
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED     3  71
  AMP PEAK 12(8Q24.21) WILD-TYPE   2 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      3   71
  AMP PEAK 12(8Q24.21) WILD-TYPE    2  149
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            149
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(11Q22.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q22.2) MUTATED    18  18
  AMP PEAK 13(11Q22.2) WILD-TYPE 141  80
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            36                            221 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            18                             80 
$`AMP PEAK 13(11Q22.2) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB2X TCGA-FX-A3NK 
       34.68        17.95        14.43       106.45        13.28        16.60 
TCGA-HB-A43Z TCGA-IE-A4EH TCGA-KF-A41W TCGA-PC-A5DP TCGA-3B-A9HI TCGA-DX-A1KX 
       37.02        26.93        11.70        18.08        50.01        68.61 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A2J1 TCGA-DX-A3LT 
       54.21        85.02         5.26        27.81        95.38        49.05 
TCGA-DX-A3M1 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YQ 
       44.68        45.99        24.26        35.28        15.95         3.06 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-AATS 
       50.50        16.87        64.21        21.30         9.34         1.15 
TCGA-DX-AB2Q TCGA-FX-A3TO TCGA-HS-A5N8 TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A8VH 
       66.74        20.32         0.72        13.08        18.08        10.52 

$`AMP PEAK 13(11Q22.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 
       15.22        14.07        15.85        40.60        12.07        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 
      101.98        30.51        60.00        84.66        32.15        12.62 
TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       52.11        52.27        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        12.85        45.11        18.54        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ 
       74.66        76.41        66.87         6.28        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
        9.70        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI 
       26.99        41.00        78.28        86.30       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S 
       17.79        12.00        15.72        65.98        86.10         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        21.70        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88         4.57        33.30         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01        17.65         1.84        46.82        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        64.77         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        84.79        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       35.18        19.17        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                          0.72                           0.49 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                        106.45                         188.15 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                         22.78                          31.96 
[1] "0.7 - 106.5 (22.8)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.6"
D13V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 13(11Q22.2) MUTATED                0                  1
  AMP PEAK 13(11Q22.2) WILD-TYPE              1                  6
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 13(11Q22.2) MUTATED                     0                   0
  AMP PEAK 13(11Q22.2) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 13(11Q22.2) MUTATED                               1
  AMP PEAK 13(11Q22.2) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 13(11Q22.2) MUTATED                       0                      4
  AMP PEAK 13(11Q22.2) WILD-TYPE                     1                     24
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 13(11Q22.2) MUTATED                      1                    0
  AMP PEAK 13(11Q22.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 13(11Q22.2) MUTATED                                       0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 13(11Q22.2) MUTATED                                  0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 13(11Q22.2) MUTATED                                                0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 13(11Q22.2) MUTATED                                 1
  AMP PEAK 13(11Q22.2) WILD-TYPE                               9
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 13(11Q22.2) MUTATED                                         0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 13(11Q22.2) MUTATED                              0
  AMP PEAK 13(11Q22.2) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 13(11Q22.2) MUTATED                         0
  AMP PEAK 13(11Q22.2) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 13(11Q22.2) MUTATED                                  4
  AMP PEAK 13(11Q22.2) WILD-TYPE                               13
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 13(11Q22.2) MUTATED                                         1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                       4
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 13(11Q22.2) MUTATED                              6
  AMP PEAK 13(11Q22.2) WILD-TYPE                           38
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 13(11Q22.2) MUTATED                                         0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 13(11Q22.2) MUTATED                                           1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 13(11Q22.2) MUTATED                                                  0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 13(11Q22.2) MUTATED                                          0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                        8
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 13(11Q22.2) MUTATED                                                         0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 13(11Q22.2) MUTATED                                            0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 13(11Q22.2) MUTATED                                                  12
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                61
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 13(11Q22.2) MUTATED                                                    0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 13(11Q22.2) MUTATED                                    1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 13(11Q22.2) MUTATED                          0
  AMP PEAK 13(11Q22.2) WILD-TYPE                        5
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 13(11Q22.2) MUTATED                             0
  AMP PEAK 13(11Q22.2) WILD-TYPE                           4
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 13(11Q22.2) MUTATED                           0
  AMP PEAK 13(11Q22.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 13(11Q22.2) MUTATED                                   1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                 6
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 13(11Q22.2) MUTATED                                   2
  AMP PEAK 13(11Q22.2) WILD-TYPE                                 3
D13V3, multiclass
                                                         clus
vv                                                        AMP PEAK 13(11Q22.2) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 1
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             4
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            1
  LOWER EXTREMITY - THIGH/KNEE                                                       6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                                        0
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        AMP PEAK 13(11Q22.2) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   6
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              24
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              4
  LOWER EXTREMITY - THIGH/KNEE                                                        38
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                                          4
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q22.2) MUTATED    18  18
  AMP PEAK 13(11Q22.2) WILD-TYPE 121 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q22.2) MUTATED     18   18
  AMP PEAK 13(11Q22.2) WILD-TYPE  121  100
        clus
vv       AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE
  FEMALE                           18                            121
  MALE                             18                            100
[1] 2 2
[1] FALSE
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q22.2) MUTATED    23  13
  AMP PEAK 13(11Q22.2) WILD-TYPE 156  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q22.2) MUTATED     23   13
  AMP PEAK 13(11Q22.2) WILD-TYPE  156   59
     clus
vv    AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE
  NO                            23                            156
  YES                           13                             59
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 13(11Q22.2) MUTATED                             13             0
  AMP PEAK 13(11Q22.2) WILD-TYPE                           46             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 13(11Q22.2) MUTATED                                                                          0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 13(11Q22.2) MUTATED                      8
  AMP PEAK 13(11Q22.2) WILD-TYPE                   95
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 13(11Q22.2) MUTATED                                                  1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                8
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 13(11Q22.2) MUTATED                  5
  AMP PEAK 13(11Q22.2) WILD-TYPE               19
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 13(11Q22.2) MUTATED                                                          8
  AMP PEAK 13(11Q22.2) WILD-TYPE                                                       20
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 13(11Q22.2) MUTATED                                          0
  AMP PEAK 13(11Q22.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 13(11Q22.2) MUTATED                             0
  AMP PEAK 13(11Q22.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 13(11Q22.2) MUTATED                               0
  AMP PEAK 13(11Q22.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 13(11Q22.2) MUTATED                                            1
  AMP PEAK 13(11Q22.2) WILD-TYPE                                         20
D13V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 13(11Q22.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       13
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                                8
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    1
  MYXOFIBROSARCOMA                                                                                    5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          1
                                                                          clus
vv                                                                         AMP PEAK 13(11Q22.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         46
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      8
  MYXOFIBROSARCOMA                                                                                     19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(11Q22.2) MUTATED    20  10   2   4
  AMP PEAK 13(11Q22.2) WILD-TYPE 132  59   7  22
D13V7, multiclass
    clus
vv   AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE
  R0                           20                            132
  R1                           10                             59
  R2                            2                              7
  RX                            4                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11Q22.2) MUTATED       0                         0    33
  AMP PEAK 13(11Q22.2) WILD-TYPE     6                        18   191
D13V8, multiclass
                           clus
vv                          AMP PEAK 13(11Q22.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               33
                           clus
vv                          AMP PEAK 13(11Q22.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q22.2) MUTATED     1  31
  AMP PEAK 13(11Q22.2) WILD-TYPE   4 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q22.2) MUTATED      1   31
  AMP PEAK 13(11Q22.2) WILD-TYPE    4  189
                        clus
vv                       AMP PEAK 13(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK 13(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q15) MUTATION ANALYSIS
D14V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 14(12Q15) MUTATED    52  42
  AMP PEAK 14(12Q15) WILD-TYPE 107  56
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          94                          163 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          42                           56 
$`AMP PEAK 14(12Q15) MUTATED`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       36.30        31.53        34.68        14.43        15.85        40.60 
TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      106.45        30.51        60.00        84.66        32.15        16.60 
TCGA-HS-A5N9 TCGA-KF-A41W TCGA-QC-A6FX TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HL 
       52.11        11.70        20.94        17.52        35.08        19.69 
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ 
       44.91         0.56        14.04        32.71        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A48N 
      136.44        33.44        44.68        31.86        35.77        35.28 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YX 
       28.96        31.96        36.85        26.99        41.00        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL 
       86.30        64.21        34.49        20.05         9.34        45.14 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2S 
       40.77        19.43         1.15        12.00        15.72         9.21 
TCGA-DX-AB2V TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ 
      106.55        49.15        20.32         4.57         0.72         3.22 
TCGA-IF-A3RQ TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.12        10.45        37.55        38.63        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       35.90       111.98        10.52        16.77         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-X6-A7W8 
       25.35        32.75        13.41        10.72        11.93        26.43 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A973 TCGA-Z4-AAPF 
       19.17        20.65        36.43        15.95 

$`AMP PEAK 14(12Q15) WILD-TYPE`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG 
       16.18        67.20        34.36        75.32        15.22        17.95 
TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A43Z 
       14.07        12.07        13.28        22.85       101.98        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-VT-A80J 
       17.75         8.28         6.35        18.08       188.15        26.17 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       41.49        50.01        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A23U TCGA-DX-A3U7 TCGA-DX-A3U8 
       18.64        26.56        68.61        76.41        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       85.45         9.73        45.99        24.26        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z2 
       82.68        36.33         3.06        78.28        50.50       101.23 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       61.97        47.87        38.17       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2L TCGA-DX-AB2O 
       36.69        60.66         6.58        17.79        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       66.74        77.88        50.40        50.89        71.31        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       21.70        19.89        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ 
       33.30         9.80        80.48        19.53         1.38        19.89 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       17.36        23.38         5.19        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DO 
       17.98        22.39        11.57         7.36       122.96        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VD 
       13.08        17.65         1.84        46.82        37.12       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       64.77         0.72        18.94         8.61        19.63        13.22 
TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46         4.80        84.79        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        8.58        63.35        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.18        50.86        29.46        27.32         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                        0.56                         0.49 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                      136.44                       188.15 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                      31.695                       30.840 
[1] "0.6 - 136.4 (31.7)" "0.5 - 188.2 (30.8)"
[1] "hr=" "1.5"
D14V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 14(12Q15) MUTATED                0                  4
  AMP PEAK 14(12Q15) WILD-TYPE              1                  3
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 14(12Q15) MUTATED                     0                   0
  AMP PEAK 14(12Q15) WILD-TYPE                   2                   1
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 14(12Q15) MUTATED                               1
  AMP PEAK 14(12Q15) WILD-TYPE                             1
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 14(12Q15) MUTATED                       0                      3
  AMP PEAK 14(12Q15) WILD-TYPE                     1                     25
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 14(12Q15) MUTATED                      0                    0
  AMP PEAK 14(12Q15) WILD-TYPE                    2                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 14(12Q15) MUTATED                                       0
  AMP PEAK 14(12Q15) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 14(12Q15) MUTATED                                  0
  AMP PEAK 14(12Q15) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 14(12Q15) MUTATED                                                0
  AMP PEAK 14(12Q15) WILD-TYPE                                              2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 14(12Q15) MUTATED                                 3
  AMP PEAK 14(12Q15) WILD-TYPE                               7
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 14(12Q15) MUTATED                                         1
  AMP PEAK 14(12Q15) WILD-TYPE                                       1
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 14(12Q15) MUTATED                              0
  AMP PEAK 14(12Q15) WILD-TYPE                            4
                              vv
clus                           LOWER EXTREMITY - GROIN
  AMP PEAK 14(12Q15) MUTATED                         2
  AMP PEAK 14(12Q15) WILD-TYPE                       0
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 14(12Q15) MUTATED                                  4
  AMP PEAK 14(12Q15) WILD-TYPE                               13
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 14(12Q15) MUTATED                                         2
  AMP PEAK 14(12Q15) WILD-TYPE                                       3
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 14(12Q15) MUTATED                              9
  AMP PEAK 14(12Q15) WILD-TYPE                           35
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 14(12Q15) MUTATED                                         0
  AMP PEAK 14(12Q15) WILD-TYPE                                       4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 14(12Q15) MUTATED                                           1
  AMP PEAK 14(12Q15) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 14(12Q15) MUTATED                                                  3
  AMP PEAK 14(12Q15) WILD-TYPE                                                2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 14(12Q15) MUTATED                                          2
  AMP PEAK 14(12Q15) WILD-TYPE                                        6
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 14(12Q15) MUTATED                                                         1
  AMP PEAK 14(12Q15) WILD-TYPE                                                       1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 14(12Q15) MUTATED                                            0
  AMP PEAK 14(12Q15) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 14(12Q15) MUTATED                                                  47
  AMP PEAK 14(12Q15) WILD-TYPE                                                26
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 14(12Q15) MUTATED                                                    0
  AMP PEAK 14(12Q15) WILD-TYPE                                                  3
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 14(12Q15) MUTATED                                    1
  AMP PEAK 14(12Q15) WILD-TYPE                                  1
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  AMP PEAK 14(12Q15) MUTATED                          3
  AMP PEAK 14(12Q15) WILD-TYPE                        2
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 14(12Q15) MUTATED                             0
  AMP PEAK 14(12Q15) WILD-TYPE                           4
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  AMP PEAK 14(12Q15) MUTATED                           0
  AMP PEAK 14(12Q15) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 14(12Q15) MUTATED                                   3
  AMP PEAK 14(12Q15) WILD-TYPE                                 4
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 14(12Q15) MUTATED                                   3
  AMP PEAK 14(12Q15) WILD-TYPE                                 2
D14V3, multiclass
                                                         clus
vv                                                        AMP PEAK 14(12Q15) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               4
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              0
  CHEST - OTHER (PLEASE SPECIFY                                                    1
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                           3
  HEAD AND NECK - HEAD                                                             0
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          1
  LOWER EXTREMITY - FOOT/ANKLE                                                     0
  LOWER EXTREMITY - GROIN                                                          2
  LOWER EXTREMITY - LOWER LEG/CALF                                                 4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          2
  LOWER EXTREMITY - THIGH/KNEE                                                     9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               47
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               1
  SUPERFICIAL TRUNK - BACK                                                         3
  SUPERFICIAL TRUNK - BUTTOCK                                                      0
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                3
                                                         clus
vv                                                        AMP PEAK 14(12Q15) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            25
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            1
  LOWER EXTREMITY - FOOT/ANKLE                                                       4
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 26
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                              cls
clus                             0   1
  AMP PEAK 14(12Q15) MUTATED    37  57
  AMP PEAK 14(12Q15) WILD-TYPE 102  61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(12Q15) MUTATED     37   57
  AMP PEAK 14(12Q15) WILD-TYPE  102   61
        clus
vv       AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE
  FEMALE                         37                          102
  MALE                           57                           61
[1] 2 2
[1] FALSE
D14V5, binary
                              cls
clus                             0   1
  AMP PEAK 14(12Q15) MUTATED    68  25
  AMP PEAK 14(12Q15) WILD-TYPE 111  47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(12Q15) MUTATED     68   25
  AMP PEAK 14(12Q15) WILD-TYPE  111   47
     clus
vv    AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE
  NO                          68                          111
  YES                         25                           47
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 14(12Q15) MUTATED                             52             0
  AMP PEAK 14(12Q15) WILD-TYPE                            7             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 14(12Q15) MUTATED                                                                          0
  AMP PEAK 14(12Q15) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  AMP PEAK 14(12Q15) MUTATED                     10
  AMP PEAK 14(12Q15) WILD-TYPE                   93
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 14(12Q15) MUTATED                                                  5
  AMP PEAK 14(12Q15) WILD-TYPE                                                4
                              vv
clus                           MYXOFIBROSARCOMA
  AMP PEAK 14(12Q15) MUTATED                  9
  AMP PEAK 14(12Q15) WILD-TYPE               15
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 14(12Q15) MUTATED                                                          9
  AMP PEAK 14(12Q15) WILD-TYPE                                                       19
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 14(12Q15) MUTATED                                          1
  AMP PEAK 14(12Q15) WILD-TYPE                                        1
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 14(12Q15) MUTATED                             0
  AMP PEAK 14(12Q15) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 14(12Q15) MUTATED                               0
  AMP PEAK 14(12Q15) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 14(12Q15) MUTATED                                            8
  AMP PEAK 14(12Q15) WILD-TYPE                                         13
D14V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 14(12Q15) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     52
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             10
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  5
  MYXOFIBROSARCOMA                                                                                  9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          1
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        8
                                                                          clus
vv                                                                         AMP PEAK 14(12Q15) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        7
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               93
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    4
  MYXOFIBROSARCOMA                                                                                   15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            1
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 14(12Q15) MUTATED    42  38   4   9
  AMP PEAK 14(12Q15) WILD-TYPE 110  31   5  17
D14V7, multiclass
    clus
vv   AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE
  R0                         42                          110
  R1                         38                           31
  R2                          4                            5
  RX                          9                           17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q15) MUTATED       3                         1    86
  AMP PEAK 14(12Q15) WILD-TYPE     3                        17   138
D14V8, multiclass
                           clus
vv                          AMP PEAK 14(12Q15) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             86
                           clus
vv                          AMP PEAK 14(12Q15) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                              cls
clus                             0   1
  AMP PEAK 14(12Q15) MUTATED     2  84
  AMP PEAK 14(12Q15) WILD-TYPE   3 136
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(12Q15) MUTATED      2   84
  AMP PEAK 14(12Q15) WILD-TYPE    3  136
                        clus
vv                       AMP PEAK 14(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       AMP PEAK 14(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          136
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q34) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(13Q34) MUTATED    30  24
  AMP PEAK 15(13Q34) WILD-TYPE 129  74
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          54                          203 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          24                           74 
$`AMP PEAK 15(13Q34) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2P TCGA-HS-A5N9 TCGA-IF-A4AK 
       16.18        34.36        17.95        12.07        52.11        52.27 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-3B-A9HI TCGA-3B-A9HR 
       11.70        17.75         6.35        18.08        50.01        88.57 
TCGA-3B-A9HV TCGA-DX-A23R TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 
       14.37        74.66        14.99        24.26        35.28        15.95 
TCGA-DX-A6BB TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN 
       36.33        41.00        50.50        61.97        47.87        38.17 
TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2Z 
       27.95        60.66        12.00        86.10        77.88        50.40 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VE TCGA-K1-A6RU TCGA-K1-A6RV 
       19.89       171.09        13.58        16.41        23.38         5.19 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-RN-AAAQ 
       14.99         7.36        37.55        17.65        48.59        16.77 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
       18.94        22.82         8.61        22.62         8.58        26.43 
TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPF 
       18.08        35.18        50.86        27.32        36.43        15.95 

$`AMP PEAK 15(13Q34) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        67.20        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X 
       14.43        14.07        15.85        40.60       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       16.60        37.02        12.62        26.93        28.21       159.29 
TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
       22.62         8.28        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS 
       41.49        35.08        19.69        53.49        68.55        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       18.64        26.56         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       66.94         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O 
       50.43        34.88        85.45         9.73        45.99        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       82.68        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       20.05         9.34        45.14        40.77       150.35        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
       36.69        19.43         6.58         1.15        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        66.74         9.21       106.55        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       49.15        31.13        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       25.22        85.97         5.92         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33        62.17       123.78        17.36        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        22.39        11.57        10.45       122.96        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        13.08         1.84        46.82        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        25.35        32.75        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       65.46        63.35        35.90        45.34        30.84        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       20.65        29.46         4.37        13.38        15.98 

  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                        5.19                         0.49 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      171.09                       188.15 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                       23.82                        32.15 
[1] "5.2 - 171.1 (23.8)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.4"
D15V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 15(13Q34) MUTATED                0                  3
  AMP PEAK 15(13Q34) WILD-TYPE              1                  4
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 15(13Q34) MUTATED                     0                   0
  AMP PEAK 15(13Q34) WILD-TYPE                   2                   1
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 15(13Q34) MUTATED                               0
  AMP PEAK 15(13Q34) WILD-TYPE                             2
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 15(13Q34) MUTATED                       0                      8
  AMP PEAK 15(13Q34) WILD-TYPE                     1                     20
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 15(13Q34) MUTATED                      0                    0
  AMP PEAK 15(13Q34) WILD-TYPE                    2                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 15(13Q34) MUTATED                                       0
  AMP PEAK 15(13Q34) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 15(13Q34) MUTATED                                  0
  AMP PEAK 15(13Q34) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 15(13Q34) MUTATED                                                2
  AMP PEAK 15(13Q34) WILD-TYPE                                              0
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 15(13Q34) MUTATED                                 3
  AMP PEAK 15(13Q34) WILD-TYPE                               7
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 15(13Q34) MUTATED                                         0
  AMP PEAK 15(13Q34) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 15(13Q34) MUTATED                              0
  AMP PEAK 15(13Q34) WILD-TYPE                            4
                              vv
clus                           LOWER EXTREMITY - GROIN
  AMP PEAK 15(13Q34) MUTATED                         1
  AMP PEAK 15(13Q34) WILD-TYPE                       1
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 15(13Q34) MUTATED                                  4
  AMP PEAK 15(13Q34) WILD-TYPE                               13
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 15(13Q34) MUTATED                                         2
  AMP PEAK 15(13Q34) WILD-TYPE                                       3
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 15(13Q34) MUTATED                             16
  AMP PEAK 15(13Q34) WILD-TYPE                           28
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 15(13Q34) MUTATED                                         0
  AMP PEAK 15(13Q34) WILD-TYPE                                       4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 15(13Q34) MUTATED                                           0
  AMP PEAK 15(13Q34) WILD-TYPE                                         2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 15(13Q34) MUTATED                                                  0
  AMP PEAK 15(13Q34) WILD-TYPE                                                5
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 15(13Q34) MUTATED                                          0
  AMP PEAK 15(13Q34) WILD-TYPE                                        8
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 15(13Q34) MUTATED                                                         0
  AMP PEAK 15(13Q34) WILD-TYPE                                                       2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 15(13Q34) MUTATED                                            0
  AMP PEAK 15(13Q34) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 15(13Q34) MUTATED                                                   7
  AMP PEAK 15(13Q34) WILD-TYPE                                                66
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 15(13Q34) MUTATED                                                    1
  AMP PEAK 15(13Q34) WILD-TYPE                                                  2
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 15(13Q34) MUTATED                                    0
  AMP PEAK 15(13Q34) WILD-TYPE                                  2
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  AMP PEAK 15(13Q34) MUTATED                          0
  AMP PEAK 15(13Q34) WILD-TYPE                        5
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 15(13Q34) MUTATED                             2
  AMP PEAK 15(13Q34) WILD-TYPE                           2
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  AMP PEAK 15(13Q34) MUTATED                           0
  AMP PEAK 15(13Q34) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 15(13Q34) MUTATED                                   3
  AMP PEAK 15(13Q34) WILD-TYPE                                 4
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 15(13Q34) MUTATED                                   2
  AMP PEAK 15(13Q34) WILD-TYPE                                 3
D15V3, multiclass
                                                         clus
vv                                                        AMP PEAK 15(13Q34) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               3
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              0
  CHEST - OTHER (PLEASE SPECIFY                                                    0
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                           8
  HEAD AND NECK - HEAD                                                             0
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     0
  LOWER EXTREMITY - GROIN                                                          1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          2
  LOWER EXTREMITY - THIGH/KNEE                                                    16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                7
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               0
  SUPERFICIAL TRUNK - BACK                                                         0
  SUPERFICIAL TRUNK - BUTTOCK                                                      2
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                2
                                                         clus
vv                                                        AMP PEAK 15(13Q34) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            20
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       4
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 66
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           5
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED    35  19
  AMP PEAK 15(13Q34) WILD-TYPE 104  99
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED     35   19
  AMP PEAK 15(13Q34) WILD-TYPE  104   99
        clus
vv       AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  FEMALE                         35                          104
  MALE                           19                           99
[1] 2 2
[1] FALSE
D15V5, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED    32  22
  AMP PEAK 15(13Q34) WILD-TYPE 147  50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED     32   22
  AMP PEAK 15(13Q34) WILD-TYPE  147   50
     clus
vv    AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  NO                          32                          147
  YES                         22                           50
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 15(13Q34) MUTATED                              5             0
  AMP PEAK 15(13Q34) WILD-TYPE                           54             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 15(13Q34) MUTATED                                                                          0
  AMP PEAK 15(13Q34) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  AMP PEAK 15(13Q34) MUTATED                     23
  AMP PEAK 15(13Q34) WILD-TYPE                   80
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 15(13Q34) MUTATED                                                  2
  AMP PEAK 15(13Q34) WILD-TYPE                                                7
                              vv
clus                           MYXOFIBROSARCOMA
  AMP PEAK 15(13Q34) MUTATED                  8
  AMP PEAK 15(13Q34) WILD-TYPE               16
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 15(13Q34) MUTATED                                                          9
  AMP PEAK 15(13Q34) WILD-TYPE                                                       19
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 15(13Q34) MUTATED                                          1
  AMP PEAK 15(13Q34) WILD-TYPE                                        1
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 15(13Q34) MUTATED                             0
  AMP PEAK 15(13Q34) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 15(13Q34) MUTATED                               0
  AMP PEAK 15(13Q34) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 15(13Q34) MUTATED                                            6
  AMP PEAK 15(13Q34) WILD-TYPE                                         15
D15V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 15(13Q34) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      5
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  2
  MYXOFIBROSARCOMA                                                                                  8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          1
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        6
                                                                          clus
vv                                                                         AMP PEAK 15(13Q34) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       54
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    7
  MYXOFIBROSARCOMA                                                                                   16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            1
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         15
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 15(13Q34) MUTATED    28  17   1   7
  AMP PEAK 15(13Q34) WILD-TYPE 124  52   8  19
D15V7, multiclass
    clus
vv   AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  R0                         28                          124
  R1                         17                           52
  R2                          1                            8
  RX                          7                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q34) MUTATED       0                         8    45
  AMP PEAK 15(13Q34) WILD-TYPE     6                        10   179
D15V8, multiclass
                           clus
vv                          AMP PEAK 15(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          8
  WHITE                                             45
                           clus
vv                          AMP PEAK 15(13Q34) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     0  49
  AMP PEAK 15(13Q34) WILD-TYPE   5 171
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      0   49
  AMP PEAK 15(13Q34) WILD-TYPE    5  171
                        clus
vv                       AMP PEAK 15(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         49
                        clus
vv                       AMP PEAK 15(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          171
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(15Q26.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.3) MUTATED    49  35
  AMP PEAK 16(15Q26.3) WILD-TYPE 110  63
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            84                            173 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            35                             63 
$`AMP PEAK 16(15Q26.3) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X 
       31.53        67.20        15.22        12.07       106.45        13.28 
TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-PC-A5DP 
       30.51        16.60        37.02        12.62        52.27        18.08 
TCGA-SG-A849 TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX 
       17.52        19.69        68.55        88.57        44.91        42.84 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       36.03        26.56        14.04        32.71        68.61        18.54 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       74.66         6.28         8.58        51.02        14.99        68.55 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       85.45        24.26        82.68         3.06        41.00        78.28 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BO 
       16.87        86.30        64.21        34.49        61.97        40.77 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A3RE 
       19.43         1.15        12.00        66.74       106.55        21.70 
TCGA-FX-A3TO TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
       20.32        19.53         3.22        19.89        25.22       171.09 
TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-LI-A67I 
       13.58         3.91        62.17        23.38        63.81        30.31 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       21.73        14.99        37.55        81.01        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       35.90       111.98        10.52        16.77        18.94         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XS 
       25.35        32.75         8.61        19.63        13.41        84.79 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A971 TCGA-Z4-AAPG 
        8.58        26.43        45.34        19.17        27.32        15.98 

$`AMP PEAK 16(15Q26.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        34.68        16.18        34.36        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 
       14.43        14.07        15.85        40.60        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 
       60.00        84.66        32.15        52.11        26.93        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
      159.29        22.62        11.70        17.75         8.28         6.35 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
       20.94       188.15        26.17        41.49        35.08        50.01 
TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        54.74        25.25        14.37        10.32        38.47 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       18.64         0.56        12.85        45.11        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        73.87        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EF 
       31.96        36.85        26.99        50.50       101.23        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS 
        9.34        45.14        47.87        38.17       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G 
       40.44        36.69        60.66         6.58        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B 
       65.98        86.10         9.21        77.88        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        49.15        31.13        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       80.48         1.38        37.12        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
        1.05       101.26        53.33       123.78        17.36         5.19 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       16.41        35.28        25.41         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN 
       22.39        11.57        10.45         7.36       122.96        38.63 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
       13.08        17.65         1.84        48.59        37.12       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71O TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D 
       64.77         0.72        22.82        13.22        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       11.93         4.80        38.27        65.46        22.62        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       35.90        18.08        30.84        35.18        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          1.15                           0.49 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                        171.09                         188.15 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                         25.89                          33.44 
[1] "1.1 - 171.1 (25.9)" "0.5 - 188.2 (33.4)"
[1] "hr=" "1.2"
D16V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 16(15Q26.3) MUTATED                0                  2
  AMP PEAK 16(15Q26.3) WILD-TYPE              1                  5
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 16(15Q26.3) MUTATED                     0                   0
  AMP PEAK 16(15Q26.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 16(15Q26.3) MUTATED                               1
  AMP PEAK 16(15Q26.3) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 16(15Q26.3) MUTATED                       1                      6
  AMP PEAK 16(15Q26.3) WILD-TYPE                     0                     22
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 16(15Q26.3) MUTATED                      0                    0
  AMP PEAK 16(15Q26.3) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 16(15Q26.3) MUTATED                                       0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 16(15Q26.3) MUTATED                                  0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 16(15Q26.3) MUTATED                                                2
  AMP PEAK 16(15Q26.3) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 16(15Q26.3) MUTATED                                 2
  AMP PEAK 16(15Q26.3) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 16(15Q26.3) MUTATED                                         0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 16(15Q26.3) MUTATED                              0
  AMP PEAK 16(15Q26.3) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 16(15Q26.3) MUTATED                         0
  AMP PEAK 16(15Q26.3) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 16(15Q26.3) MUTATED                                  7
  AMP PEAK 16(15Q26.3) WILD-TYPE                               10
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 16(15Q26.3) MUTATED                                         2
  AMP PEAK 16(15Q26.3) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 16(15Q26.3) MUTATED                             21
  AMP PEAK 16(15Q26.3) WILD-TYPE                           23
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 16(15Q26.3) MUTATED                                         1
  AMP PEAK 16(15Q26.3) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 16(15Q26.3) MUTATED                                           2
  AMP PEAK 16(15Q26.3) WILD-TYPE                                         0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 16(15Q26.3) MUTATED                                                  1
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 16(15Q26.3) MUTATED                                          2
  AMP PEAK 16(15Q26.3) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 16(15Q26.3) MUTATED                                                         0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 16(15Q26.3) MUTATED                                            1
  AMP PEAK 16(15Q26.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 16(15Q26.3) MUTATED                                                  25
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                48
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 16(15Q26.3) MUTATED                                                    0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 16(15Q26.3) MUTATED                                    1
  AMP PEAK 16(15Q26.3) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 16(15Q26.3) MUTATED                          1
  AMP PEAK 16(15Q26.3) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 16(15Q26.3) MUTATED                             1
  AMP PEAK 16(15Q26.3) WILD-TYPE                           3
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 16(15Q26.3) MUTATED                           0
  AMP PEAK 16(15Q26.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 16(15Q26.3) MUTATED                                   3
  AMP PEAK 16(15Q26.3) WILD-TYPE                                 4
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 16(15Q26.3) MUTATED                                   1
  AMP PEAK 16(15Q26.3) WILD-TYPE                                 4
D16V3, multiclass
                                                         clus
vv                                                        AMP PEAK 16(15Q26.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                             6
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                      21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 25
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        1
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        AMP PEAK 16(15Q26.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   5
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              22
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   48
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          3
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                                cls
clus                              0  1
  AMP PEAK 16(15Q26.3) MUTATED   50 34
  AMP PEAK 16(15Q26.3) WILD-TYPE 89 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED     50   34
  AMP PEAK 16(15Q26.3) WILD-TYPE   89   84
        clus
vv       AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  FEMALE                           50                             89
  MALE                             34                             84
[1] 2 2
[1] FALSE
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED    56  27
  AMP PEAK 16(15Q26.3) WILD-TYPE 123  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED     56   27
  AMP PEAK 16(15Q26.3) WILD-TYPE  123   45
     clus
vv    AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  NO                            56                            123
  YES                           27                             45
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 16(15Q26.3) MUTATED                             15             0
  AMP PEAK 16(15Q26.3) WILD-TYPE                           44             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 16(15Q26.3) MUTATED                                                                          0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 16(15Q26.3) MUTATED                     33
  AMP PEAK 16(15Q26.3) WILD-TYPE                   70
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 16(15Q26.3) MUTATED                                                  5
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                4
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 16(15Q26.3) MUTATED                 12
  AMP PEAK 16(15Q26.3) WILD-TYPE               12
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 16(15Q26.3) MUTATED                                                         11
  AMP PEAK 16(15Q26.3) WILD-TYPE                                                       17
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 16(15Q26.3) MUTATED                                          0
  AMP PEAK 16(15Q26.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 16(15Q26.3) MUTATED                             0
  AMP PEAK 16(15Q26.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 16(15Q26.3) MUTATED                               0
  AMP PEAK 16(15Q26.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 16(15Q26.3) MUTATED                                            8
  AMP PEAK 16(15Q26.3) WILD-TYPE                                         13
D16V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 16(15Q26.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       15
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               33
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    5
  MYXOFIBROSARCOMA                                                                                   12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          8
                                                                          clus
vv                                                                         AMP PEAK 16(15Q26.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         44
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 70
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      4
  MYXOFIBROSARCOMA                                                                                     12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(15Q26.3) MUTATED    46  24   2  11
  AMP PEAK 16(15Q26.3) WILD-TYPE 106  45   7  15
D16V7, multiclass
    clus
vv   AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  R0                           46                            106
  R1                           24                             45
  R2                            2                              7
  RX                           11                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.3) MUTATED       2                         4    76
  AMP PEAK 16(15Q26.3) WILD-TYPE     4                        14   148
D16V8, multiclass
                           clus
vv                          AMP PEAK 16(15Q26.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               76
                           clus
vv                          AMP PEAK 16(15Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     3  76
  AMP PEAK 16(15Q26.3) WILD-TYPE   2 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      3   76
  AMP PEAK 16(15Q26.3) WILD-TYPE    2  144
                        clus
vv                       AMP PEAK 16(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       AMP PEAK 16(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17P12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(17P12) MUTATED    57  45
  AMP PEAK 17(17P12) WILD-TYPE 102  53
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                         102                          155 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                          45                           53 
$`AMP PEAK 17(17P12) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-AB2P 
       34.68        16.18        67.20        75.32        17.95        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
      106.45        13.28        84.66        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-SG-A849 
       52.27        11.70        17.75         6.35        18.08        17.52 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       35.08        50.01        19.69        68.55        88.57        44.91 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW 
       42.84        10.32        38.47        26.56         0.56        32.71 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U5 TCGA-DX-A3UC 
       12.85        54.21        85.02         6.28        31.86        68.55 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        85.45        45.99        24.26        35.28        52.77 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YV TCGA-DX-A7EM 
       26.47        15.95        82.68         3.06        50.50        62.20 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BV 
        9.34        45.14        47.87        38.17        27.95        60.66 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       86.10        77.88       106.55        21.70        20.32        19.89 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ 
       34.88         4.57        33.30        80.48         3.22        19.89 
TCGA-IF-A4AJ TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
       25.22         3.91       101.26         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-A7B5 
       35.28        30.31        10.45         7.36        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 
       17.65        46.82        18.08        37.12        16.77        18.94 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS 
       22.82        25.35         8.61        13.41        10.72        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62         8.58        26.43        35.90        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-Z4-AAPG 
       35.18        19.17        20.65        50.86        27.32        15.98 

$`AMP PEAK 17(17P12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        31.53        34.36        15.22        14.43        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       15.85        40.60        22.85       101.98        30.51        60.00 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       32.15        16.60        37.02        28.21       159.29        22.62 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP 
        8.28        20.94       188.15        26.17        41.49        53.49 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU 
       54.74        25.25        14.37        36.03        18.64        14.04 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       68.61        45.11        18.54        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      136.44        33.44        44.68        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48P 
       14.99        10.68        73.87        50.43         9.73        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
      108.82        59.84        37.58        37.41        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX 
       31.96        36.85        26.99        41.00        78.28        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       86.30        64.21       101.23        21.30        34.49        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BO 
      152.12        29.49        48.20        20.05        61.97        40.77 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
      150.35        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
       17.79        12.00        15.72        65.98        66.74         9.21 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       50.40        50.89        71.31        49.15        31.13        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK 
        8.05        67.63         0.72         9.80        19.53         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       37.12       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        1.05        53.33        62.17       123.78        17.36        23.38 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 
       22.39        11.57       122.96        37.55        38.63         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        35.90       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-AB3D 
        0.72         3.88        32.75        19.63        13.22        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WB 
       11.93         4.80        38.27        65.46        63.35        18.08 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                        0.56                         0.49 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                      106.55                       188.15 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                      27.635                       32.150 
[1] "0.6 - 106.5 (27.6)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.4"
D17V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 17(17P12) MUTATED                0                  2
  AMP PEAK 17(17P12) WILD-TYPE              1                  5
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 17(17P12) MUTATED                     0                   1
  AMP PEAK 17(17P12) WILD-TYPE                   2                   0
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 17(17P12) MUTATED                               1
  AMP PEAK 17(17P12) WILD-TYPE                             1
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 17(17P12) MUTATED                       1                     12
  AMP PEAK 17(17P12) WILD-TYPE                     0                     16
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 17(17P12) MUTATED                      1                    0
  AMP PEAK 17(17P12) WILD-TYPE                    1                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 17(17P12) MUTATED                                       0
  AMP PEAK 17(17P12) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 17(17P12) MUTATED                                  0
  AMP PEAK 17(17P12) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 17(17P12) MUTATED                                                0
  AMP PEAK 17(17P12) WILD-TYPE                                              2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 17(17P12) MUTATED                                 1
  AMP PEAK 17(17P12) WILD-TYPE                               9
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 17(17P12) MUTATED                                         0
  AMP PEAK 17(17P12) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 17(17P12) MUTATED                              1
  AMP PEAK 17(17P12) WILD-TYPE                            3
                              vv
clus                           LOWER EXTREMITY - GROIN
  AMP PEAK 17(17P12) MUTATED                         0
  AMP PEAK 17(17P12) WILD-TYPE                       2
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 17(17P12) MUTATED                                 10
  AMP PEAK 17(17P12) WILD-TYPE                                7
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 17(17P12) MUTATED                                         4
  AMP PEAK 17(17P12) WILD-TYPE                                       1
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 17(17P12) MUTATED                             22
  AMP PEAK 17(17P12) WILD-TYPE                           22
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 17(17P12) MUTATED                                         1
  AMP PEAK 17(17P12) WILD-TYPE                                       3
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 17(17P12) MUTATED                                           1
  AMP PEAK 17(17P12) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 17(17P12) MUTATED                                                  1
  AMP PEAK 17(17P12) WILD-TYPE                                                4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 17(17P12) MUTATED                                          2
  AMP PEAK 17(17P12) WILD-TYPE                                        6
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 17(17P12) MUTATED                                                         1
  AMP PEAK 17(17P12) WILD-TYPE                                                       1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 17(17P12) MUTATED                                            0
  AMP PEAK 17(17P12) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 17(17P12) MUTATED                                                  27
  AMP PEAK 17(17P12) WILD-TYPE                                                46
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 17(17P12) MUTATED                                                    1
  AMP PEAK 17(17P12) WILD-TYPE                                                  2
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 17(17P12) MUTATED                                    0
  AMP PEAK 17(17P12) WILD-TYPE                                  2
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  AMP PEAK 17(17P12) MUTATED                          2
  AMP PEAK 17(17P12) WILD-TYPE                        3
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 17(17P12) MUTATED                             2
  AMP PEAK 17(17P12) WILD-TYPE                           2
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  AMP PEAK 17(17P12) MUTATED                           0
  AMP PEAK 17(17P12) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 17(17P12) MUTATED                                   5
  AMP PEAK 17(17P12) WILD-TYPE                                 2
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 17(17P12) MUTATED                                   2
  AMP PEAK 17(17P12) WILD-TYPE                                 3
D17V3, multiclass
                                                         clus
vv                                                        AMP PEAK 17(17P12) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               2
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              1
  CHEST - OTHER (PLEASE SPECIFY                                                    1
  GYNECOLOGICAL - OVARY                                                            1
  GYNECOLOGICAL - UTERUS                                                          12
  HEAD AND NECK - HEAD                                                             1
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     1
  LOWER EXTREMITY - GROIN                                                          0
  LOWER EXTREMITY - LOWER LEG/CALF                                                10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          4
  LOWER EXTREMITY - THIGH/KNEE                                                    22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               0
  SUPERFICIAL TRUNK - BACK                                                         2
  SUPERFICIAL TRUNK - BUTTOCK                                                      2
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                2
                                                         clus
vv                                                        AMP PEAK 17(17P12) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 5
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                            16
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       3
  LOWER EXTREMITY - GROIN                                                            2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            1
  LOWER EXTREMITY - THIGH/KNEE                                                      22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           3
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                              cls
clus                            0  1
  AMP PEAK 17(17P12) MUTATED   57 45
  AMP PEAK 17(17P12) WILD-TYPE 82 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17P12) MUTATED     57   45
  AMP PEAK 17(17P12) WILD-TYPE   82   73
        clus
vv       AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE
  FEMALE                         57                           82
  MALE                           45                           73
[1] 2 2
[1] FALSE
D17V5, binary
                              cls
clus                             0   1
  AMP PEAK 17(17P12) MUTATED    64  36
  AMP PEAK 17(17P12) WILD-TYPE 115  36
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17P12) MUTATED     64   36
  AMP PEAK 17(17P12) WILD-TYPE  115   36
     clus
vv    AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE
  NO                          64                          115
  YES                         36                           36
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 17(17P12) MUTATED                             14             0
  AMP PEAK 17(17P12) WILD-TYPE                           45             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 17(17P12) MUTATED                                                                          0
  AMP PEAK 17(17P12) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  AMP PEAK 17(17P12) MUTATED                     48
  AMP PEAK 17(17P12) WILD-TYPE                   55
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 17(17P12) MUTATED                                                  3
  AMP PEAK 17(17P12) WILD-TYPE                                                6
                              vv
clus                           MYXOFIBROSARCOMA
  AMP PEAK 17(17P12) MUTATED                 11
  AMP PEAK 17(17P12) WILD-TYPE               13
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 17(17P12) MUTATED                                                         12
  AMP PEAK 17(17P12) WILD-TYPE                                                       16
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 17(17P12) MUTATED                                          0
  AMP PEAK 17(17P12) WILD-TYPE                                        2
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 17(17P12) MUTATED                             0
  AMP PEAK 17(17P12) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 17(17P12) MUTATED                               0
  AMP PEAK 17(17P12) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 17(17P12) MUTATED                                           14
  AMP PEAK 17(17P12) WILD-TYPE                                          7
D17V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 17(17P12) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     14
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             48
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  3
  MYXOFIBROSARCOMA                                                                                 11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          0
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                       14
                                                                          clus
vv                                                                         AMP PEAK 17(17P12) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       45
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               55
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            2
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 17(17P12) MUTATED   56 30  3 12
  AMP PEAK 17(17P12) WILD-TYPE 96 39  6 14
D17V7, multiclass
    clus
vv   AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE
  R0                         56                           96
  R1                         30                           39
  R2                          3                            6
  RX                         12                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17P12) MUTATED       3                         6    88
  AMP PEAK 17(17P12) WILD-TYPE     3                        12   136
D17V8, multiclass
                           clus
vv                          AMP PEAK 17(17P12) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             88
                           clus
vv                          AMP PEAK 17(17P12) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  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"
D17V9, binary
                              cls
clus                             0   1
  AMP PEAK 17(17P12) MUTATED     1  94
  AMP PEAK 17(17P12) WILD-TYPE   4 126
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17P12) MUTATED      1   94
  AMP PEAK 17(17P12) WILD-TYPE    4  126
                        clus
vv                       AMP PEAK 17(17P12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         94
                        clus
vv                       AMP PEAK 17(17P12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          126
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(17P11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(17P11.2) MUTATED    59  45
  AMP PEAK 18(17P11.2) WILD-TYPE 100  53
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                           104                            153 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                            45                             53 
$`AMP PEAK 18(17P11.2) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       34.68        16.18        67.20        34.36        75.32        17.95 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-HB-A5W3 TCGA-HS-A5N9 
       12.07       106.45        13.28        84.66        12.62        52.11 
TCGA-IE-A4EH TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-SG-A849 
       26.93        11.70        17.75         6.35        18.08        17.52 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HY 
       35.08        50.01        88.57        44.91        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 
       38.47        26.56         0.56        32.71        12.85        85.02 
TCGA-DX-A23Y TCGA-DX-A3U5 TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
        6.28        31.86        68.55        34.88        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ 
       24.26        26.47        15.95        82.68        36.33         3.06 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BK 
       41.00        50.50        86.30        62.20         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BV 
       45.14        47.87        38.17        40.77        27.95        60.66 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       86.10        66.74       106.55        21.70        20.32        19.89 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
       34.88         4.57        33.30         3.22        19.89        25.22 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
        3.91       101.26         5.19        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DO 
       30.31        25.41        21.73        10.45         7.36        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VH 
       13.08        17.65        46.82        18.08        48.59        10.52 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
       18.94        22.82        25.35         8.61        13.41        10.72 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA 
       84.79        65.46        22.62         8.58        26.43        35.90 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`AMP PEAK 18(17P11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        15.22        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A 
       40.60        22.85       101.98        30.51        60.00        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       16.60        37.02        52.27        28.21       159.29        22.62 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HL 
        8.28        20.94       188.15        26.17        41.49        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9I0 
       53.49        68.55        54.74        25.25        14.37        36.03 
TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       18.64        14.04        68.61        45.11        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       50.43         9.73        35.28        52.77        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       59.84        37.58        37.41        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       26.99        78.28        16.87        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
      150.35        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T 
       17.79        12.00        15.72        65.98         9.21        77.88 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       50.40        50.89        71.31        49.15        31.13        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        8.05        67.63         0.72         9.80        80.48        19.53 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
        1.38        37.12       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         1.05        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       23.38         0.49        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VC 
       11.57       122.96        37.55        38.63         1.84        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        64.77         0.72        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-AB3D TCGA-WK-A8XO 
        3.88        32.75        19.63        13.22        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C7 TCGA-X9-A973 
        4.80        38.27        63.35        18.08        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                        106.55                         188.15 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                        27.635                         32.150 
[1] "0.6 - 106.5 (27.6)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.3"
D18V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 18(17P11.2) MUTATED                0                  4
  AMP PEAK 18(17P11.2) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 18(17P11.2) MUTATED                     0                   1
  AMP PEAK 18(17P11.2) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 18(17P11.2) MUTATED                               2
  AMP PEAK 18(17P11.2) WILD-TYPE                             0
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 18(17P11.2) MUTATED                       1                     12
  AMP PEAK 18(17P11.2) WILD-TYPE                     0                     16
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 18(17P11.2) MUTATED                      1                    0
  AMP PEAK 18(17P11.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 18(17P11.2) MUTATED                                       0
  AMP PEAK 18(17P11.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 18(17P11.2) MUTATED                                  0
  AMP PEAK 18(17P11.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 18(17P11.2) MUTATED                                                0
  AMP PEAK 18(17P11.2) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 18(17P11.2) MUTATED                                 2
  AMP PEAK 18(17P11.2) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 18(17P11.2) MUTATED                                         0
  AMP PEAK 18(17P11.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 18(17P11.2) MUTATED                              0
  AMP PEAK 18(17P11.2) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 18(17P11.2) MUTATED                         1
  AMP PEAK 18(17P11.2) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 18(17P11.2) MUTATED                                 13
  AMP PEAK 18(17P11.2) WILD-TYPE                                4
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 18(17P11.2) MUTATED                                         4
  AMP PEAK 18(17P11.2) WILD-TYPE                                       1
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 18(17P11.2) MUTATED                             22
  AMP PEAK 18(17P11.2) WILD-TYPE                           22
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 18(17P11.2) MUTATED                                         1
  AMP PEAK 18(17P11.2) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 18(17P11.2) MUTATED                                           1
  AMP PEAK 18(17P11.2) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 18(17P11.2) MUTATED                                                  1
  AMP PEAK 18(17P11.2) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 18(17P11.2) MUTATED                                          2
  AMP PEAK 18(17P11.2) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 18(17P11.2) MUTATED                                                         1
  AMP PEAK 18(17P11.2) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 18(17P11.2) MUTATED                                            0
  AMP PEAK 18(17P11.2) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 18(17P11.2) MUTATED                                                  22
  AMP PEAK 18(17P11.2) WILD-TYPE                                                51
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 18(17P11.2) MUTATED                                                    2
  AMP PEAK 18(17P11.2) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 18(17P11.2) MUTATED                                    0
  AMP PEAK 18(17P11.2) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 18(17P11.2) MUTATED                          2
  AMP PEAK 18(17P11.2) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 18(17P11.2) MUTATED                             2
  AMP PEAK 18(17P11.2) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 18(17P11.2) MUTATED                           0
  AMP PEAK 18(17P11.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 18(17P11.2) MUTATED                                   4
  AMP PEAK 18(17P11.2) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 18(17P11.2) MUTATED                                   2
  AMP PEAK 18(17P11.2) WILD-TYPE                                 3
D18V3, multiclass
                                                         clus
vv                                                        AMP PEAK 18(17P11.2) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            12
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            4
  LOWER EXTREMITY - THIGH/KNEE                                                      22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        AMP PEAK 18(17P11.2) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        0
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              16
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              1
  LOWER EXTREMITY - THIGH/KNEE                                                        22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   51
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                                cls
clus                              0  1
  AMP PEAK 18(17P11.2) MUTATED   61 43
  AMP PEAK 18(17P11.2) WILD-TYPE 78 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17P11.2) MUTATED     61   43
  AMP PEAK 18(17P11.2) WILD-TYPE   78   75
        clus
vv       AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE
  FEMALE                           61                             78
  MALE                             43                             75
[1] 2 2
[1] FALSE
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(17P11.2) MUTATED    60  42
  AMP PEAK 18(17P11.2) WILD-TYPE 119  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17P11.2) MUTATED     60   42
  AMP PEAK 18(17P11.2) WILD-TYPE  119   30
     clus
vv    AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE
  NO                            60                            119
  YES                           42                             30
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 18(17P11.2) MUTATED                             11             0
  AMP PEAK 18(17P11.2) WILD-TYPE                           48             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 18(17P11.2) MUTATED                                                                          0
  AMP PEAK 18(17P11.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 18(17P11.2) MUTATED                     46
  AMP PEAK 18(17P11.2) WILD-TYPE                   57
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 18(17P11.2) MUTATED                                                  3
  AMP PEAK 18(17P11.2) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 18(17P11.2) MUTATED                 13
  AMP PEAK 18(17P11.2) WILD-TYPE               11
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 18(17P11.2) MUTATED                                                         16
  AMP PEAK 18(17P11.2) WILD-TYPE                                                       12
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 18(17P11.2) MUTATED                                          0
  AMP PEAK 18(17P11.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 18(17P11.2) MUTATED                             0
  AMP PEAK 18(17P11.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 18(17P11.2) MUTATED                               0
  AMP PEAK 18(17P11.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 18(17P11.2) MUTATED                                           15
  AMP PEAK 18(17P11.2) WILD-TYPE                                          6
D18V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 18(17P11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       11
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               46
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         15
                                                                          clus
vv                                                                         AMP PEAK 18(17P11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         48
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 57
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 18(17P11.2) MUTATED   55 32  3 14
  AMP PEAK 18(17P11.2) WILD-TYPE 97 37  6 12
D18V7, multiclass
    clus
vv   AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE
  R0                           55                             97
  R1                           32                             37
  R2                            3                              6
  RX                           14                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17P11.2) MUTATED       3                         5    91
  AMP PEAK 18(17P11.2) WILD-TYPE     3                        13   133
D18V8, multiclass
                           clus
vv                          AMP PEAK 18(17P11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               91
                           clus
vv                          AMP PEAK 18(17P11.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(17P11.2) MUTATED     2  94
  AMP PEAK 18(17P11.2) WILD-TYPE   3 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17P11.2) MUTATED      2   94
  AMP PEAK 18(17P11.2) WILD-TYPE    3  126
                        clus
vv                       AMP PEAK 18(17P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 18(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            126
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(17Q24.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q24.3) MUTATED    46  33
  AMP PEAK 19(17Q24.3) WILD-TYPE 113  65
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            79                            178 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            33                             65 
$`AMP PEAK 19(17Q24.3) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 
       16.18        34.36        17.95       106.45        13.28        84.66 
TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-LI-A9QH TCGA-PC-A5DP 
       32.15        37.02        12.62        52.11        17.75        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HQ TCGA-3B-A9HT 
       20.94       188.15        17.52        50.01        68.55        54.74 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1L2 
       42.84        18.64        26.56         0.56        32.71        85.02 
TCGA-DX-A2J0 TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BF TCGA-DX-A6YS 
        9.70        44.68        10.68        45.99        31.96        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BN 
       50.50        16.87        86.30        21.30        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       40.77        60.66         1.15        77.88       106.55        50.40 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 
       49.15        21.70        19.89        67.63         4.57         0.72 
TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J TCGA-KD-A5QS TCGA-KD-A5QT 
       19.89        13.58        85.97         3.91        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5VA 
       35.28        30.31        10.45         7.36        13.08        18.08 
TCGA-QQ-A5VC TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
       35.90        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS 
       32.75         8.61        19.63        13.41        10.72        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 
       22.62         8.58        63.35        26.43        35.18        19.17 
TCGA-X9-A971 
       27.32 

$`AMP PEAK 19(17Q24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        67.20        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 
       14.43        14.07        15.85        40.60        12.07        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK TCGA-IE-A4EH TCGA-IF-A4AK 
      101.98        30.51        60.00        16.60        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM 
       28.21       159.29        22.62        11.70         8.28         6.35 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR 
       26.17        41.49        35.08        19.69        53.49        88.57 
TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       44.91        25.25        14.37        10.32        38.47        36.03 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         8.58        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 
        9.04        49.05        86.83       136.44        33.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       50.43        34.88        85.45         9.73        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       15.95        37.41        82.68        36.33        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       26.99         3.06        41.00        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
        9.34        61.97        45.14       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        19.43         6.58        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        86.10        66.74         9.21        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 
       31.13        20.32        15.48         8.05        34.88        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
       25.22       171.09         5.92        16.41         1.05       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57       122.96        37.55        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
       17.65         1.84        46.82        48.59        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-VT-AB3D 
      111.98        64.77        10.52         0.72        13.22        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7WA TCGA-X6-A7WB 
       11.93         4.80        38.27        65.46        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       45.34        30.84        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                        188.15                         171.09 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                         26.43                          33.37 
[1] "0.6 - 188.2 (26.4)" "0.5 - 171.1 (33.4)"
[1] "hr=" "1.3"
D19V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 19(17Q24.3) MUTATED                0                  3
  AMP PEAK 19(17Q24.3) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 19(17Q24.3) MUTATED                     0                   0
  AMP PEAK 19(17Q24.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 19(17Q24.3) MUTATED                               0
  AMP PEAK 19(17Q24.3) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 19(17Q24.3) MUTATED                       1                     14
  AMP PEAK 19(17Q24.3) WILD-TYPE                     0                     14
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 19(17Q24.3) MUTATED                      1                    0
  AMP PEAK 19(17Q24.3) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 19(17Q24.3) MUTATED                                       1
  AMP PEAK 19(17Q24.3) WILD-TYPE                                     1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 19(17Q24.3) MUTATED                                  0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 19(17Q24.3) MUTATED                                                0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 19(17Q24.3) MUTATED                                 0
  AMP PEAK 19(17Q24.3) WILD-TYPE                              10
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 19(17Q24.3) MUTATED                                         0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 19(17Q24.3) MUTATED                              1
  AMP PEAK 19(17Q24.3) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 19(17Q24.3) MUTATED                         0
  AMP PEAK 19(17Q24.3) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 19(17Q24.3) MUTATED                                  6
  AMP PEAK 19(17Q24.3) WILD-TYPE                               11
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 19(17Q24.3) MUTATED                                         3
  AMP PEAK 19(17Q24.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 19(17Q24.3) MUTATED                             18
  AMP PEAK 19(17Q24.3) WILD-TYPE                           26
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 19(17Q24.3) MUTATED                                         1
  AMP PEAK 19(17Q24.3) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 19(17Q24.3) MUTATED                                           1
  AMP PEAK 19(17Q24.3) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 19(17Q24.3) MUTATED                                                  1
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 19(17Q24.3) MUTATED                                          3
  AMP PEAK 19(17Q24.3) WILD-TYPE                                        5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 19(17Q24.3) MUTATED                                                         1
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 19(17Q24.3) MUTATED                                            0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 19(17Q24.3) MUTATED                                                  14
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                59
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 19(17Q24.3) MUTATED                                                    0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 19(17Q24.3) MUTATED                                    0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 19(17Q24.3) MUTATED                          2
  AMP PEAK 19(17Q24.3) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 19(17Q24.3) MUTATED                             2
  AMP PEAK 19(17Q24.3) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 19(17Q24.3) MUTATED                           0
  AMP PEAK 19(17Q24.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 19(17Q24.3) MUTATED                                   3
  AMP PEAK 19(17Q24.3) WILD-TYPE                                 4
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 19(17Q24.3) MUTATED                                   2
  AMP PEAK 19(17Q24.3) WILD-TYPE                                 3
D19V3, multiclass
                                                         clus
vv                                                        AMP PEAK 19(17Q24.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            14
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        AMP PEAK 19(17Q24.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              14
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.3) MUTATED   51 28
  AMP PEAK 19(17Q24.3) WILD-TYPE 88 90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED     51   28
  AMP PEAK 19(17Q24.3) WILD-TYPE   88   90
        clus
vv       AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  FEMALE                           51                             88
  MALE                             28                             90
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.3) MUTATED    48  30
  AMP PEAK 19(17Q24.3) WILD-TYPE 131  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED     48   30
  AMP PEAK 19(17Q24.3) WILD-TYPE  131   42
     clus
vv    AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  NO                            48                            131
  YES                           30                             42
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 19(17Q24.3) MUTATED                             13             0
  AMP PEAK 19(17Q24.3) WILD-TYPE                           46             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 19(17Q24.3) MUTATED                                                                          0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 19(17Q24.3) MUTATED                     27
  AMP PEAK 19(17Q24.3) WILD-TYPE                   76
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 19(17Q24.3) MUTATED                                                  6
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 19(17Q24.3) MUTATED                 12
  AMP PEAK 19(17Q24.3) WILD-TYPE               12
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 19(17Q24.3) MUTATED                                                         12
  AMP PEAK 19(17Q24.3) WILD-TYPE                                                       16
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 19(17Q24.3) MUTATED                                          0
  AMP PEAK 19(17Q24.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 19(17Q24.3) MUTATED                             0
  AMP PEAK 19(17Q24.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 19(17Q24.3) MUTATED                               0
  AMP PEAK 19(17Q24.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 19(17Q24.3) MUTATED                                            9
  AMP PEAK 19(17Q24.3) WILD-TYPE                                         12
D19V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 19(17Q24.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       13
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          9
                                                                          clus
vv                                                                         AMP PEAK 19(17Q24.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         46
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                     12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(17Q24.3) MUTATED    42  18   5  13
  AMP PEAK 19(17Q24.3) WILD-TYPE 110  51   4  13
D19V7, multiclass
    clus
vv   AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  R0                           42                            110
  R1                           18                             51
  R2                            5                              4
  RX                           13                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q24.3) MUTATED       3                         5    66
  AMP PEAK 19(17Q24.3) WILD-TYPE     3                        13   158
D19V8, multiclass
                           clus
vv                          AMP PEAK 19(17Q24.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               66
                           clus
vv                          AMP PEAK 19(17Q24.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.3) MUTATED     1  69
  AMP PEAK 19(17Q24.3) WILD-TYPE   4 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED      1   69
  AMP PEAK 19(17Q24.3) WILD-TYPE    4  151
                        clus
vv                       AMP PEAK 19(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK 19(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            151
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(19P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(19P13.2) MUTATED   65 43
  AMP PEAK 20(19P13.2) WILD-TYPE 94 55
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           108                            149 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            43                             55 
$`AMP PEAK 20(19P13.2) MUTATED`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        34.68        67.20        75.32        15.22        14.43 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 
      106.45        13.28        30.51        32.15        16.60        52.11 
TCGA-LI-A9QH TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HI 
       17.75        20.94       188.15        17.52        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HX 
       19.69        53.49        88.57        44.91        14.37        42.84 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       36.03        18.64         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23Y 
       12.85        54.21        85.02        33.53        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
        9.70       136.44        31.86        51.02        14.99        50.43 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6YR 
       85.45        35.28        37.58        37.41        82.68        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        50.50        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ES TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       34.49        62.20        20.05        45.14        47.87        40.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2O 
       27.95        40.44        36.69        19.43        17.79        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       66.74        77.88       106.55        21.70        20.32        19.89 
TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        4.57         9.80        80.48        19.53         3.22         1.38 
TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
        3.91        62.17       123.78        63.81        16.41        35.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-N1-A6IA TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        0.49        21.73        14.99         7.36        46.82        18.08 
TCGA-QQ-A5VC TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       35.90        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX 
       13.22        13.41        10.72        12.46        84.79        38.27 
TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPG 
        8.58        18.08        45.34        27.32        36.43        15.98 

$`AMP PEAK 20(19P13.2) WILD-TYPE`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H 
       31.53        16.18        34.36        17.95        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
       40.60        12.07        22.85       101.98        60.00        84.66 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        12.62        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-VT-A80J 
       22.62        11.70         8.28         6.35        18.08        26.17 
TCGA-WK-A8XT TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       41.49        68.55        54.74        25.25        10.32        38.47 
TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       26.56        45.11        18.54        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81        60.30         8.58        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 
        9.04        49.05        86.83        33.44        44.68        35.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        73.87        68.55        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        24.26        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       59.84        15.95        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       26.99         3.06        16.87        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BV 
       48.20         9.34        61.97        38.17       150.35        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S 
        6.58         1.15        12.00        15.72        65.98         9.21 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       50.40        50.89        71.31        49.15        31.13        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A6BZ 
        8.05        67.63        34.88        33.30         0.72        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       37.12        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU 
       16.41         1.05       101.26        53.33        17.36        23.38 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
        5.19        30.31        25.41        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       11.57        10.45       122.96        37.55        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
       13.08        17.65         1.84        48.59        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        3.88        11.93         4.80        65.46        22.62        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        35.90        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       50.86        29.46         4.37        13.38        15.95 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.49                           0.72 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                        188.15                         171.09 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         34.01                          29.46 
[1] "0.5 - 188.2 (34.0)" "0.7 - 171.1 (29.5)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 20(19P13.2) MUTATED                0                  2
  AMP PEAK 20(19P13.2) WILD-TYPE              1                  5
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 20(19P13.2) MUTATED                     0                   0
  AMP PEAK 20(19P13.2) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 20(19P13.2) MUTATED                               0
  AMP PEAK 20(19P13.2) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 20(19P13.2) MUTATED                       1                     13
  AMP PEAK 20(19P13.2) WILD-TYPE                     0                     15
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 20(19P13.2) MUTATED                      1                    0
  AMP PEAK 20(19P13.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 20(19P13.2) MUTATED                                       0
  AMP PEAK 20(19P13.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 20(19P13.2) MUTATED                                  0
  AMP PEAK 20(19P13.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 20(19P13.2) MUTATED                                                2
  AMP PEAK 20(19P13.2) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 20(19P13.2) MUTATED                                 3
  AMP PEAK 20(19P13.2) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 20(19P13.2) MUTATED                                         0
  AMP PEAK 20(19P13.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 20(19P13.2) MUTATED                              0
  AMP PEAK 20(19P13.2) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 20(19P13.2) MUTATED                         1
  AMP PEAK 20(19P13.2) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 20(19P13.2) MUTATED                                  5
  AMP PEAK 20(19P13.2) WILD-TYPE                               12
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 20(19P13.2) MUTATED                                         3
  AMP PEAK 20(19P13.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 20(19P13.2) MUTATED                             21
  AMP PEAK 20(19P13.2) WILD-TYPE                           23
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 20(19P13.2) MUTATED                                         4
  AMP PEAK 20(19P13.2) WILD-TYPE                                       0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 20(19P13.2) MUTATED                                           2
  AMP PEAK 20(19P13.2) WILD-TYPE                                         0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 20(19P13.2) MUTATED                                                  0
  AMP PEAK 20(19P13.2) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 20(19P13.2) MUTATED                                          3
  AMP PEAK 20(19P13.2) WILD-TYPE                                        5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 20(19P13.2) MUTATED                                                         1
  AMP PEAK 20(19P13.2) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 20(19P13.2) MUTATED                                            1
  AMP PEAK 20(19P13.2) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 20(19P13.2) MUTATED                                                  31
  AMP PEAK 20(19P13.2) WILD-TYPE                                                42
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 20(19P13.2) MUTATED                                                    0
  AMP PEAK 20(19P13.2) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 20(19P13.2) MUTATED                                    2
  AMP PEAK 20(19P13.2) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 20(19P13.2) MUTATED                          2
  AMP PEAK 20(19P13.2) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 20(19P13.2) MUTATED                             1
  AMP PEAK 20(19P13.2) WILD-TYPE                           3
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 20(19P13.2) MUTATED                           0
  AMP PEAK 20(19P13.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 20(19P13.2) MUTATED                                   5
  AMP PEAK 20(19P13.2) WILD-TYPE                                 2
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 20(19P13.2) MUTATED                                   3
  AMP PEAK 20(19P13.2) WILD-TYPE                                 2
D20V3, multiclass
                                                         clus
vv                                                        AMP PEAK 20(19P13.2) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            13
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 31
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        1
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        AMP PEAK 20(19P13.2) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   5
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              15
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   42
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          3
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   54 54
  AMP PEAK 20(19P13.2) WILD-TYPE 85 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     54   54
  AMP PEAK 20(19P13.2) WILD-TYPE   85   64
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           54                             85
  MALE                             54                             64
[1] 2 2
[1] FALSE
D20V5, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    74  31
  AMP PEAK 20(19P13.2) WILD-TYPE 105  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     74   31
  AMP PEAK 20(19P13.2) WILD-TYPE  105   41
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                            74                            105
  YES                           31                             41
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 20(19P13.2) MUTATED                             24             0
  AMP PEAK 20(19P13.2) WILD-TYPE                           35             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 20(19P13.2) MUTATED                                                                          0
  AMP PEAK 20(19P13.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 20(19P13.2) MUTATED                     40
  AMP PEAK 20(19P13.2) WILD-TYPE                   63
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 20(19P13.2) MUTATED                                                  5
  AMP PEAK 20(19P13.2) WILD-TYPE                                                4
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 20(19P13.2) MUTATED                 10
  AMP PEAK 20(19P13.2) WILD-TYPE               14
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 20(19P13.2) MUTATED                                                         17
  AMP PEAK 20(19P13.2) WILD-TYPE                                                       11
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 20(19P13.2) MUTATED                                          0
  AMP PEAK 20(19P13.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 20(19P13.2) MUTATED                             0
  AMP PEAK 20(19P13.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 20(19P13.2) MUTATED                               0
  AMP PEAK 20(19P13.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 20(19P13.2) MUTATED                                           12
  AMP PEAK 20(19P13.2) WILD-TYPE                                          9
D20V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 20(19P13.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       24
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               40
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    5
  MYXOFIBROSARCOMA                                                                                   10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         12
                                                                          clus
vv                                                                         AMP PEAK 20(19P13.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         35
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 63
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      4
  MYXOFIBROSARCOMA                                                                                     14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(19P13.2) MUTATED   61 29  4 14
  AMP PEAK 20(19P13.2) WILD-TYPE 91 40  5 12
D20V7, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  R0                           61                             91
  R1                           29                             40
  R2                            4                              5
  RX                           14                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19P13.2) MUTATED       2                         9    93
  AMP PEAK 20(19P13.2) WILD-TYPE     4                         9   131
D20V8, multiclass
                           clus
vv                          AMP PEAK 20(19P13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               93
                           clus
vv                          AMP PEAK 20(19P13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED     3  95
  AMP PEAK 20(19P13.2) WILD-TYPE   2 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      3   95
  AMP PEAK 20(19P13.2) WILD-TYPE    2  125
                        clus
vv                       AMP PEAK 20(19P13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       AMP PEAK 20(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            125
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(19Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(19Q12) MUTATED    52  41
  AMP PEAK 21(19Q12) WILD-TYPE 107  57
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          93                          164 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          41                           57 
$`AMP PEAK 21(19Q12) MUTATED`
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2X TCGA-DX-AB35 
       67.20        34.36        15.22        17.95        13.28        30.51 
TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       32.15        12.62        11.70        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HV 
       20.94        26.17        50.01        19.69        88.57        14.37 
TCGA-3B-A9HX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 
       42.84        14.04        32.71        68.61        12.85        54.21 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U9 
       85.02        74.66         6.28        49.05        51.02        14.99 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B8 
       68.55        85.45        45.99        35.28        26.47        15.95 
TCGA-DX-A6B9 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ 
       37.41         3.06        41.00        78.28        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       64.21        34.49        62.20        61.97        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       38.17        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2V TCGA-FX-A2QS TCGA-FX-A3TO 
        1.15        17.79        86.10       106.55        49.15        20.32 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        4.57         0.72         9.80        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KD-A5QS 
       19.89        13.58         5.92         1.05         5.19        63.81 
TCGA-LI-A67I TCGA-MB-A8JK TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF 
       30.31        21.73        18.08        48.59        35.90       111.98 
TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU 
       10.52        18.94        22.82        25.35         8.61        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB 
       10.72        12.46        11.93        84.79        38.27         8.58 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A973 
       45.34        19.17        36.43 

$`AMP PEAK 21(19Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BH 
       36.30        31.53        34.68        16.18        75.32        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       14.07        15.85        40.60        12.07       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 
      101.98        60.00        84.66        16.60        37.02        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 
       26.93        52.27        28.21       159.29        22.62         8.28 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ 
      188.15        17.52        41.49        35.08        53.49        68.55 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       44.91        54.74        25.25        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       18.64        26.56         0.56        45.11        18.54        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        95.38        79.17         9.04        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
      136.44        33.44        44.68        31.86        35.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L 
       10.68        73.87        50.43        34.88         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA 
       52.77        46.03       108.82        59.84        37.58        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YX 
       36.33        28.96        31.96        36.85        26.99        16.87 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        21.30        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AB2F 
       20.05         9.34        40.77       150.35         6.58        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z 
       15.72        65.98        66.74         9.21        77.88        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31        31.13        21.70        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IF-A3RQ 
        8.05        67.63        34.88        33.30        80.48        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       25.22       171.09        85.97        16.41         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT 
       53.33        62.17       123.78        17.36        23.38        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       35.28        25.41         0.49        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
       37.12       130.32        64.77         0.72        16.77         3.88 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 
       32.75        19.63        13.22         4.80        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        27.32         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                        0.72                         0.49 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                      111.98                       188.15 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                      26.470                       32.355 
[1] "0.7 - 112.0 (26.5)" "0.5 - 188.2 (32.4)"
[1] "hr=" "1.4"
D21V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 21(19Q12) MUTATED                0                  2
  AMP PEAK 21(19Q12) WILD-TYPE              1                  5
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 21(19Q12) MUTATED                     0                   0
  AMP PEAK 21(19Q12) WILD-TYPE                   2                   1
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 21(19Q12) MUTATED                               1
  AMP PEAK 21(19Q12) WILD-TYPE                             1
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 21(19Q12) MUTATED                       0                      8
  AMP PEAK 21(19Q12) WILD-TYPE                     1                     20
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 21(19Q12) MUTATED                      0                    0
  AMP PEAK 21(19Q12) WILD-TYPE                    2                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 21(19Q12) MUTATED                                       0
  AMP PEAK 21(19Q12) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 21(19Q12) MUTATED                                  0
  AMP PEAK 21(19Q12) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 21(19Q12) MUTATED                                                1
  AMP PEAK 21(19Q12) WILD-TYPE                                              1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 21(19Q12) MUTATED                                 3
  AMP PEAK 21(19Q12) WILD-TYPE                               7
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 21(19Q12) MUTATED                                         0
  AMP PEAK 21(19Q12) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 21(19Q12) MUTATED                              0
  AMP PEAK 21(19Q12) WILD-TYPE                            4
                              vv
clus                           LOWER EXTREMITY - GROIN
  AMP PEAK 21(19Q12) MUTATED                         1
  AMP PEAK 21(19Q12) WILD-TYPE                       1
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 21(19Q12) MUTATED                                  7
  AMP PEAK 21(19Q12) WILD-TYPE                               10
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 21(19Q12) MUTATED                                         5
  AMP PEAK 21(19Q12) WILD-TYPE                                       0
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 21(19Q12) MUTATED                             21
  AMP PEAK 21(19Q12) WILD-TYPE                           23
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 21(19Q12) MUTATED                                         2
  AMP PEAK 21(19Q12) WILD-TYPE                                       2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 21(19Q12) MUTATED                                           1
  AMP PEAK 21(19Q12) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 21(19Q12) MUTATED                                                  0
  AMP PEAK 21(19Q12) WILD-TYPE                                                5
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 21(19Q12) MUTATED                                          3
  AMP PEAK 21(19Q12) WILD-TYPE                                        5
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 21(19Q12) MUTATED                                                         1
  AMP PEAK 21(19Q12) WILD-TYPE                                                       1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 21(19Q12) MUTATED                                            0
  AMP PEAK 21(19Q12) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 21(19Q12) MUTATED                                                  24
  AMP PEAK 21(19Q12) WILD-TYPE                                                49
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 21(19Q12) MUTATED                                                    0
  AMP PEAK 21(19Q12) WILD-TYPE                                                  3
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 21(19Q12) MUTATED                                    1
  AMP PEAK 21(19Q12) WILD-TYPE                                  1
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  AMP PEAK 21(19Q12) MUTATED                          2
  AMP PEAK 21(19Q12) WILD-TYPE                        3
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 21(19Q12) MUTATED                             1
  AMP PEAK 21(19Q12) WILD-TYPE                           3
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  AMP PEAK 21(19Q12) MUTATED                           0
  AMP PEAK 21(19Q12) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 21(19Q12) MUTATED                                   5
  AMP PEAK 21(19Q12) WILD-TYPE                                 2
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 21(19Q12) MUTATED                                   3
  AMP PEAK 21(19Q12) WILD-TYPE                                 2
D21V3, multiclass
                                                         clus
vv                                                        AMP PEAK 21(19Q12) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               2
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              0
  CHEST - OTHER (PLEASE SPECIFY                                                    1
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                           8
  HEAD AND NECK - HEAD                                                             0
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     0
  LOWER EXTREMITY - GROIN                                                          1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          5
  LOWER EXTREMITY - THIGH/KNEE                                                    21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               24
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               1
  SUPERFICIAL TRUNK - BACK                                                         2
  SUPERFICIAL TRUNK - BUTTOCK                                                      1
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                3
                                                         clus
vv                                                        AMP PEAK 21(19Q12) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 5
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            20
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       4
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            0
  LOWER EXTREMITY - THIGH/KNEE                                                      23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 49
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           3
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                              cls
clus                            0  1
  AMP PEAK 21(19Q12) MUTATED   46 47
  AMP PEAK 21(19Q12) WILD-TYPE 93 71
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED     46   47
  AMP PEAK 21(19Q12) WILD-TYPE   93   71
        clus
vv       AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  FEMALE                         46                           93
  MALE                           47                           71
[1] 2 2
[1] FALSE
D21V5, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED    58  33
  AMP PEAK 21(19Q12) WILD-TYPE 121  39
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED     58   33
  AMP PEAK 21(19Q12) WILD-TYPE  121   39
     clus
vv    AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  NO                          58                          121
  YES                         33                           39
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 21(19Q12) MUTATED                             18             0
  AMP PEAK 21(19Q12) WILD-TYPE                           41             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 21(19Q12) MUTATED                                                                          0
  AMP PEAK 21(19Q12) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  AMP PEAK 21(19Q12) MUTATED                     32
  AMP PEAK 21(19Q12) WILD-TYPE                   71
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 21(19Q12) MUTATED                                                  3
  AMP PEAK 21(19Q12) WILD-TYPE                                                6
                              vv
clus                           MYXOFIBROSARCOMA
  AMP PEAK 21(19Q12) MUTATED                 14
  AMP PEAK 21(19Q12) WILD-TYPE               10
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 21(19Q12) MUTATED                                                         16
  AMP PEAK 21(19Q12) WILD-TYPE                                                       12
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 21(19Q12) MUTATED                                          0
  AMP PEAK 21(19Q12) WILD-TYPE                                        2
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 21(19Q12) MUTATED                             0
  AMP PEAK 21(19Q12) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 21(19Q12) MUTATED                               0
  AMP PEAK 21(19Q12) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 21(19Q12) MUTATED                                           10
  AMP PEAK 21(19Q12) WILD-TYPE                                         11
D21V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 21(19Q12) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     18
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  3
  MYXOFIBROSARCOMA                                                                                 14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          0
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                       10
                                                                          clus
vv                                                                         AMP PEAK 21(19Q12) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       41
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            2
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         11
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 21(19Q12) MUTATED    50  27   4  12
  AMP PEAK 21(19Q12) WILD-TYPE 102  42   5  14
D21V7, multiclass
    clus
vv   AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  R0                         50                          102
  R1                         27                           42
  R2                          4                            5
  RX                         12                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19Q12) MUTATED       2                         5    83
  AMP PEAK 21(19Q12) WILD-TYPE     4                        13   141
D21V8, multiclass
                           clus
vv                          AMP PEAK 21(19Q12) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             83
                           clus
vv                          AMP PEAK 21(19Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED     1  82
  AMP PEAK 21(19Q12) WILD-TYPE   4 138
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED      1   82
  AMP PEAK 21(19Q12) WILD-TYPE    4  138
                        clus
vv                       AMP PEAK 21(19Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         82
                        clus
vv                       AMP PEAK 21(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          138
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(20Q13.33) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20Q13.33) MUTATED    54  44
  AMP PEAK 22(20Q13.33) WILD-TYPE 105  54
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             98                             159 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             44                              54 
$`AMP PEAK 22(20Q13.33) MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       34.36        15.22        14.43        12.07       106.45        22.85 
TCGA-DX-AB35 TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       30.51        52.27        11.70        17.75         8.28         6.35 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94        17.52        26.17        35.08        50.01        19.69 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       88.57        44.91        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U9 
       74.66         6.28         8.58       136.44        31.86        14.99 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BB 
       10.68        35.28        46.03        59.84        15.95        36.33 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
        3.06        78.28        16.87        86.30        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS 
       34.49        61.97        45.14        47.87        40.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q 
       36.69        19.43         1.15        17.79        12.00        66.74 
TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-IE-A3OV 
      106.55        31.13        20.32        19.89         4.57        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
       19.53         3.22       171.09        13.58         5.92        16.41 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-LI-A67I TCGA-MB-A5Y8 
       62.17        23.38         5.19        63.81        30.31        25.41 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        7.36        37.55        13.08        17.65        46.82        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P 
       37.12       111.98        10.52        16.77        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-X6-A7W8 TCGA-X6-A7WB 
       32.75         8.61        13.41        10.72        26.43        18.08 
TCGA-X6-A7WC TCGA-X6-A8C3 
       45.34        19.17 

$`AMP PEAK 22(20Q13.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB32 
       17.95        14.07        15.85        40.60        13.28       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DP 
       52.11        26.93        28.21       159.29        22.62        18.08 
TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
      188.15        41.49        53.49        68.55        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       86.83        33.44        44.68        35.77        51.02         4.54 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       45.99        24.26        52.77        26.47       108.82        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        82.68        28.96        31.96        36.85        26.99 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       41.00        50.50       101.23        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BR 
       29.49        48.20        20.05         9.34        38.17       150.35 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
       40.44        60.66         6.58        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
       21.70        15.48         8.05        67.63        34.88        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        0.72         9.80         1.38        19.89        37.12        25.22 
TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       85.97         1.05         3.91       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       17.36        16.41        35.28         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK 
       14.99        17.98        22.39        11.57        10.45       122.96 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD 
       38.63        81.01         1.84        48.59        35.90       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-AA8C TCGA-UE-A6QT 
       64.77         0.72        18.94         3.88        19.63        13.22 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62         8.58        63.35        35.90        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                           0.56                            0.49 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         171.09                          188.15 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         24.365                          34.880 
[1] "0.6 - 171.1 (24.4)" "0.5 - 188.2 (34.9)"
[1] "hr=" "1.6"
D22V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 22(20Q13.33) MUTATED                0                  2
  AMP PEAK 22(20Q13.33) WILD-TYPE              1                  5
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 22(20Q13.33) MUTATED                     0                   0
  AMP PEAK 22(20Q13.33) WILD-TYPE                   2                   1
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 22(20Q13.33) MUTATED                               1
  AMP PEAK 22(20Q13.33) WILD-TYPE                             1
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 22(20Q13.33) MUTATED                       0                      8
  AMP PEAK 22(20Q13.33) WILD-TYPE                     1                     20
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 22(20Q13.33) MUTATED                      1                    0
  AMP PEAK 22(20Q13.33) WILD-TYPE                    1                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 22(20Q13.33) MUTATED                                       0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 22(20Q13.33) MUTATED                                  0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 22(20Q13.33) MUTATED                                                1
  AMP PEAK 22(20Q13.33) WILD-TYPE                                              1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 22(20Q13.33) MUTATED                                 3
  AMP PEAK 22(20Q13.33) WILD-TYPE                               7
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 22(20Q13.33) MUTATED                                         0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 22(20Q13.33) MUTATED                              2
  AMP PEAK 22(20Q13.33) WILD-TYPE                            2
                                 vv
clus                              LOWER EXTREMITY - GROIN
  AMP PEAK 22(20Q13.33) MUTATED                         0
  AMP PEAK 22(20Q13.33) WILD-TYPE                       2
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 22(20Q13.33) MUTATED                                  8
  AMP PEAK 22(20Q13.33) WILD-TYPE                                9
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 22(20Q13.33) MUTATED                                         5
  AMP PEAK 22(20Q13.33) WILD-TYPE                                       0
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 22(20Q13.33) MUTATED                             23
  AMP PEAK 22(20Q13.33) WILD-TYPE                           21
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 22(20Q13.33) MUTATED                                         0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                       4
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 22(20Q13.33) MUTATED                                           0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                         2
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 22(20Q13.33) MUTATED                                                  0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                5
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 22(20Q13.33) MUTATED                                          2
  AMP PEAK 22(20Q13.33) WILD-TYPE                                        6
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 22(20Q13.33) MUTATED                                                         0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                       2
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 22(20Q13.33) MUTATED                                            1
  AMP PEAK 22(20Q13.33) WILD-TYPE                                          0
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 22(20Q13.33) MUTATED                                                  28
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                45
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 22(20Q13.33) MUTATED                                                    0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                  3
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 22(20Q13.33) MUTATED                                    2
  AMP PEAK 22(20Q13.33) WILD-TYPE                                  0
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  AMP PEAK 22(20Q13.33) MUTATED                          2
  AMP PEAK 22(20Q13.33) WILD-TYPE                        3
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 22(20Q13.33) MUTATED                             1
  AMP PEAK 22(20Q13.33) WILD-TYPE                           3
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  AMP PEAK 22(20Q13.33) MUTATED                           0
  AMP PEAK 22(20Q13.33) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 22(20Q13.33) MUTATED                                   5
  AMP PEAK 22(20Q13.33) WILD-TYPE                                 2
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 22(20Q13.33) MUTATED                                   2
  AMP PEAK 22(20Q13.33) WILD-TYPE                                 3
D22V3, multiclass
                                                         clus
vv                                                        AMP PEAK 22(20Q13.33) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                              8
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        2
  LOWER EXTREMITY - GROIN                                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                                    8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             5
  LOWER EXTREMITY - THIGH/KNEE                                                       23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            2
  SUPERFICIAL TRUNK - BUTTOCK                                                         1
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
                                                         clus
vv                                                        AMP PEAK 22(20Q13.33) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    5
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                                         1
  GYNECOLOGICAL - OVARY                                                                 1
  GYNECOLOGICAL - UTERUS                                                               20
  HEAD AND NECK - HEAD                                                                  1
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          2
  LOWER EXTREMITY - GROIN                                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                                      9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               0
  LOWER EXTREMITY - THIGH/KNEE                                                         21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    0
  SUPERFICIAL TRUNK - BACK                                                              3
  SUPERFICIAL TRUNK - BUTTOCK                                                           3
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q13.33) MUTATED   43 55
  AMP PEAK 22(20Q13.33) WILD-TYPE 96 63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     43   55
  AMP PEAK 22(20Q13.33) WILD-TYPE   96   63
        clus
vv       AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  FEMALE                            43                              96
  MALE                              55                              63
[1] 2 2
[1] FALSE
D22V5, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.33) MUTATED    59  37
  AMP PEAK 22(20Q13.33) WILD-TYPE 120  35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     59   37
  AMP PEAK 22(20Q13.33) WILD-TYPE  120   35
     clus
vv    AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  NO                             59                             120
  YES                            37                              35
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 22(20Q13.33) MUTATED                             21             0
  AMP PEAK 22(20Q13.33) WILD-TYPE                           38             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 22(20Q13.33) MUTATED                                                                          0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  AMP PEAK 22(20Q13.33) MUTATED                     29
  AMP PEAK 22(20Q13.33) WILD-TYPE                   74
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 22(20Q13.33) MUTATED                                                  5
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                4
                                 vv
clus                              MYXOFIBROSARCOMA
  AMP PEAK 22(20Q13.33) MUTATED                 14
  AMP PEAK 22(20Q13.33) WILD-TYPE               10
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 22(20Q13.33) MUTATED                                                         17
  AMP PEAK 22(20Q13.33) WILD-TYPE                                                       11
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 22(20Q13.33) MUTATED                                          0
  AMP PEAK 22(20Q13.33) WILD-TYPE                                        2
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 22(20Q13.33) MUTATED                             0
  AMP PEAK 22(20Q13.33) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 22(20Q13.33) MUTATED                               0
  AMP PEAK 22(20Q13.33) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 22(20Q13.33) MUTATED                                           12
  AMP PEAK 22(20Q13.33) WILD-TYPE                                          9
D22V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 22(20Q13.33) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        21
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                29
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                    14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          12
                                                                          clus
vv                                                                         AMP PEAK 22(20Q13.33) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          38
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  74
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       4
  MYXOFIBROSARCOMA                                                                                      10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20Q13.33) MUTATED    49  32   3  13
  AMP PEAK 22(20Q13.33) WILD-TYPE 103  37   6  13
D22V7, multiclass
    clus
vv   AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  R0                            49                             103
  R1                            32                              37
  R2                             3                               6
  RX                            13                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q13.33) MUTATED       2                         7    86
  AMP PEAK 22(20Q13.33) WILD-TYPE     4                        11   138
D22V8, multiclass
                           clus
vv                          AMP PEAK 22(20Q13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                86
                           clus
vv                          AMP PEAK 22(20Q13.33) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.33) MUTATED     2  87
  AMP PEAK 22(20Q13.33) WILD-TYPE   3 133
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED      2   87
  AMP PEAK 22(20Q13.33) WILD-TYPE    3  133
                        clus
vv                       AMP PEAK 22(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            87
                        clus
vv                       AMP PEAK 22(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             133
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(21Q21.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(21Q21.1) MUTATED    40  33
  AMP PEAK 23(21Q21.1) WILD-TYPE 119  65
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            73                            184 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            33                             65 
$`AMP PEAK 23(21Q21.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 
       34.68        34.36        15.22       106.45        13.28        30.51 
TCGA-HS-A5N9 TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A6FX TCGA-3B-A9HI TCGA-3B-A9HS 
       52.11        11.70         6.35        20.94        50.01        44.91 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 
       42.84        18.64        32.71        68.61        12.85        54.21 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF 
        5.26        76.41         8.58       136.44        14.99        85.45 
TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS 
       45.99        15.95        36.33        31.96        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BL 
       50.50        86.30        21.30        62.20        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E 
       47.87        27.95        36.69        60.66         1.15        17.79 
TCGA-DX-AB2V TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ 
      106.55         4.57         0.72        80.48         3.22        19.89 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-K1-A6RU TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
       25.22        13.58        23.38        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QC-AA9N 
        0.49        14.99         7.36        37.55        13.08        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-A71Q 
       46.82        48.59        35.90       111.98         3.88        32.75 
TCGA-UE-A6QT TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
       13.22        38.27        22.62         8.58        26.43        45.34 
TCGA-X9-A971 
       27.32 

$`AMP PEAK 23(21Q21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 
       14.43        14.07        15.85        40.60        12.07        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
       17.75         8.28        18.08       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        19.69        53.49        68.55        88.57 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        14.37        10.32        38.47        36.03 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       26.56         0.56        14.04        45.11        18.54        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       33.53        66.94        74.66        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       86.83        33.44        44.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
      108.82        59.84        37.58        37.41        82.68        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       36.85        26.99         3.06        16.87        64.21       101.23 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX 
        9.34        38.17        40.77       150.35        40.44        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
        6.58        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK 
       67.63        34.88        33.30         9.80        19.53         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       37.12       171.09        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
        5.19        63.81        35.28        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57        10.45       122.96        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
        1.84        18.08        37.12       130.32        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
        0.72        16.77        18.94        22.82        25.35         8.61 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       84.79        65.46        63.35        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       35.18        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                          0.49                           0.56 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                        136.44                         188.15 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                         30.51                          31.33 
[1] "0.5 - 136.4 (30.5)" "0.6 - 188.2 (31.3)"
[1] "hr=" "1.4"
D23V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 23(21Q21.1) MUTATED                0                  4
  AMP PEAK 23(21Q21.1) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 23(21Q21.1) MUTATED                     0                   0
  AMP PEAK 23(21Q21.1) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 23(21Q21.1) MUTATED                               0
  AMP PEAK 23(21Q21.1) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 23(21Q21.1) MUTATED                       0                      8
  AMP PEAK 23(21Q21.1) WILD-TYPE                     1                     20
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 23(21Q21.1) MUTATED                      2                    0
  AMP PEAK 23(21Q21.1) WILD-TYPE                    0                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 23(21Q21.1) MUTATED                                       0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 23(21Q21.1) MUTATED                                  0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 23(21Q21.1) MUTATED                                                2
  AMP PEAK 23(21Q21.1) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 23(21Q21.1) MUTATED                                 3
  AMP PEAK 23(21Q21.1) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 23(21Q21.1) MUTATED                                         0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 23(21Q21.1) MUTATED                              0
  AMP PEAK 23(21Q21.1) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  AMP PEAK 23(21Q21.1) MUTATED                         1
  AMP PEAK 23(21Q21.1) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 23(21Q21.1) MUTATED                                  5
  AMP PEAK 23(21Q21.1) WILD-TYPE                               12
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 23(21Q21.1) MUTATED                                         2
  AMP PEAK 23(21Q21.1) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 23(21Q21.1) MUTATED                             15
  AMP PEAK 23(21Q21.1) WILD-TYPE                           29
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 23(21Q21.1) MUTATED                                         2
  AMP PEAK 23(21Q21.1) WILD-TYPE                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 23(21Q21.1) MUTATED                                           0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 23(21Q21.1) MUTATED                                                  0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 23(21Q21.1) MUTATED                                          2
  AMP PEAK 23(21Q21.1) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 23(21Q21.1) MUTATED                                                         0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 23(21Q21.1) MUTATED                                            0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 23(21Q21.1) MUTATED                                                  17
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                56
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 23(21Q21.1) MUTATED                                                    0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 23(21Q21.1) MUTATED                                    1
  AMP PEAK 23(21Q21.1) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  AMP PEAK 23(21Q21.1) MUTATED                          2
  AMP PEAK 23(21Q21.1) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 23(21Q21.1) MUTATED                             2
  AMP PEAK 23(21Q21.1) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  AMP PEAK 23(21Q21.1) MUTATED                           0
  AMP PEAK 23(21Q21.1) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 23(21Q21.1) MUTATED                                   4
  AMP PEAK 23(21Q21.1) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 23(21Q21.1) MUTATED                                   1
  AMP PEAK 23(21Q21.1) WILD-TYPE                                 4
D23V3, multiclass
                                                         clus
vv                                                        AMP PEAK 23(21Q21.1) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             8
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                      15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        AMP PEAK 23(21Q21.1) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              20
  HEAD AND NECK - HEAD                                                                 0
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(21Q21.1) MUTATED    33  40
  AMP PEAK 23(21Q21.1) WILD-TYPE 106  78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(21Q21.1) MUTATED     33   40
  AMP PEAK 23(21Q21.1) WILD-TYPE  106   78
        clus
vv       AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE
  FEMALE                           33                            106
  MALE                             40                             78
[1] 2 2
[1] FALSE
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(21Q21.1) MUTATED    47  24
  AMP PEAK 23(21Q21.1) WILD-TYPE 132  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(21Q21.1) MUTATED     47   24
  AMP PEAK 23(21Q21.1) WILD-TYPE  132   48
     clus
vv    AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE
  NO                            47                            132
  YES                           24                             48
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 23(21Q21.1) MUTATED                             13             0
  AMP PEAK 23(21Q21.1) WILD-TYPE                           46             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 23(21Q21.1) MUTATED                                                                          0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  AMP PEAK 23(21Q21.1) MUTATED                     28
  AMP PEAK 23(21Q21.1) WILD-TYPE                   75
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 23(21Q21.1) MUTATED                                                  1
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                8
                                vv
clus                             MYXOFIBROSARCOMA
  AMP PEAK 23(21Q21.1) MUTATED                 11
  AMP PEAK 23(21Q21.1) WILD-TYPE               13
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 23(21Q21.1) MUTATED                                                         12
  AMP PEAK 23(21Q21.1) WILD-TYPE                                                       16
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 23(21Q21.1) MUTATED                                          0
  AMP PEAK 23(21Q21.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 23(21Q21.1) MUTATED                             0
  AMP PEAK 23(21Q21.1) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 23(21Q21.1) MUTATED                               0
  AMP PEAK 23(21Q21.1) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 23(21Q21.1) MUTATED                                            8
  AMP PEAK 23(21Q21.1) WILD-TYPE                                         13
D23V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 23(21Q21.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       13
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    1
  MYXOFIBROSARCOMA                                                                                   11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          8
                                                                          clus
vv                                                                         AMP PEAK 23(21Q21.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         46
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      8
  MYXOFIBROSARCOMA                                                                                     13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(21Q21.1) MUTATED    43  19   1  10
  AMP PEAK 23(21Q21.1) WILD-TYPE 109  50   8  16
D23V7, multiclass
    clus
vv   AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE
  R0                           43                            109
  R1                           19                             50
  R2                            1                              8
  RX                           10                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(21Q21.1) MUTATED       1                         7    62
  AMP PEAK 23(21Q21.1) WILD-TYPE     5                        11   162
D23V8, multiclass
                           clus
vv                          AMP PEAK 23(21Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               62
                           clus
vv                          AMP PEAK 23(21Q21.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(21Q21.1) MUTATED     0  66
  AMP PEAK 23(21Q21.1) WILD-TYPE   5 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(21Q21.1) MUTATED      0   66
  AMP PEAK 23(21Q21.1) WILD-TYPE    5  154
                        clus
vv                       AMP PEAK 23(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 23(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            154
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(XP21.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 24(XP21.2) MUTATED   60 37
  AMP PEAK 24(XP21.2) WILD-TYPE 99 61
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           97                           160 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           37                            61 
$`AMP PEAK 24(XP21.2) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2X 
       31.53        67.20        34.36        17.95        15.85        13.28 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-PC-A5DM 
       22.85        30.51        52.11        28.21        22.62         6.35 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94        17.52        26.17        35.08        50.01        19.69 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KX 
       88.57        44.91        25.25        42.84        38.47        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3LY 
       12.85        45.11        18.54        60.30       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       44.68         4.54        10.68        68.55        34.88        85.45 
TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YV 
       24.26        15.95        82.68        36.33        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-A8BK 
       86.30        64.21        62.20        30.35         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       45.14        47.87        38.17        27.95        40.44        60.66 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Z TCGA-FX-A2QS 
       19.43         1.15        12.00        86.10        50.40        49.15 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A3OV 
       20.32        67.63        34.88         4.57        33.30        80.48 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-K1-A42W TCGA-K1-A6RV 
       19.53        19.89        37.12        13.58        62.17         5.19 
TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DN TCGA-QC-AA9N 
       63.81        25.41        14.99         7.36        38.63        17.65 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-UE-A6QU TCGA-VT-A80G 
       18.08        35.90       111.98        10.52        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA 
       12.46        84.79        38.27         8.58        26.43        35.90 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
       45.34        30.84        35.18        19.17        20.65        27.32 
TCGA-X9-A973 
       36.43 

$`AMP PEAK 24(XP21.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        34.68        16.18        75.32        15.22        14.43 
TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB36 
       14.07        40.60        12.07       106.45       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
       52.27       159.29        11.70        17.75         8.28        18.08 
TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HV 
      188.15        41.49        53.49        68.55        54.74        14.37 
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       32.71        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ 
        5.26        76.41        66.87         6.28        27.81         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD 
       31.86        35.77        51.02        14.99        73.87        50.43 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        45.99        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
      108.82        59.84        37.58        37.41        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z2 
       36.85        26.99         3.06        41.00        16.87       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       21.30        34.49       152.12        29.49        48.20        20.05 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G 
       40.77       150.35        36.69         6.58        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B 
       65.98        66.74         9.21        77.88       106.55        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        31.13        21.70        19.89        15.48         8.05 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 
        0.72         9.80         3.22         1.38        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-KD-A5QU 
       53.33       123.78        17.36        23.38        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       30.31         0.49        21.73        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 
       11.57        10.45       122.96        37.55        81.01        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
        1.84        46.82        48.59        37.12       130.32        64.77 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       32.75         8.61        19.63        13.22        11.93         4.80 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 TCGA-X6-A8C7 
       65.46        22.62        63.35        18.08        50.86        29.46 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                         1.15                          0.49 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                       136.44                        188.15 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                       33.440                        29.475 
[1] "1.1 - 136.4 (33.4)" "0.5 - 188.2 (29.5)"
[1] "hr=" "1"  
D24V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 24(XP21.2) MUTATED                0                  2
  AMP PEAK 24(XP21.2) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 24(XP21.2) MUTATED                     0                   1
  AMP PEAK 24(XP21.2) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 24(XP21.2) MUTATED                               2
  AMP PEAK 24(XP21.2) WILD-TYPE                             0
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 24(XP21.2) MUTATED                       0                      8
  AMP PEAK 24(XP21.2) WILD-TYPE                     1                     20
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 24(XP21.2) MUTATED                      0                    0
  AMP PEAK 24(XP21.2) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 24(XP21.2) MUTATED                                       0
  AMP PEAK 24(XP21.2) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 24(XP21.2) MUTATED                                  0
  AMP PEAK 24(XP21.2) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 24(XP21.2) MUTATED                                                1
  AMP PEAK 24(XP21.2) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 24(XP21.2) MUTATED                                 4
  AMP PEAK 24(XP21.2) WILD-TYPE                               6
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 24(XP21.2) MUTATED                                         2
  AMP PEAK 24(XP21.2) WILD-TYPE                                       0
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 24(XP21.2) MUTATED                              1
  AMP PEAK 24(XP21.2) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK 24(XP21.2) MUTATED                         0
  AMP PEAK 24(XP21.2) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 24(XP21.2) MUTATED                                 10
  AMP PEAK 24(XP21.2) WILD-TYPE                                7
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 24(XP21.2) MUTATED                                         3
  AMP PEAK 24(XP21.2) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 24(XP21.2) MUTATED                             20
  AMP PEAK 24(XP21.2) WILD-TYPE                           24
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 24(XP21.2) MUTATED                                         1
  AMP PEAK 24(XP21.2) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 24(XP21.2) MUTATED                                           1
  AMP PEAK 24(XP21.2) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 24(XP21.2) MUTATED                                                  1
  AMP PEAK 24(XP21.2) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 24(XP21.2) MUTATED                                          1
  AMP PEAK 24(XP21.2) WILD-TYPE                                        7
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 24(XP21.2) MUTATED                                                         1
  AMP PEAK 24(XP21.2) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 24(XP21.2) MUTATED                                            1
  AMP PEAK 24(XP21.2) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 24(XP21.2) MUTATED                                                  25
  AMP PEAK 24(XP21.2) WILD-TYPE                                                48
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 24(XP21.2) MUTATED                                                    0
  AMP PEAK 24(XP21.2) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 24(XP21.2) MUTATED                                    0
  AMP PEAK 24(XP21.2) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK 24(XP21.2) MUTATED                          2
  AMP PEAK 24(XP21.2) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 24(XP21.2) MUTATED                             2
  AMP PEAK 24(XP21.2) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK 24(XP21.2) MUTATED                           0
  AMP PEAK 24(XP21.2) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 24(XP21.2) MUTATED                                   5
  AMP PEAK 24(XP21.2) WILD-TYPE                                 2
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 24(XP21.2) MUTATED                                   3
  AMP PEAK 24(XP21.2) WILD-TYPE                                 2
D24V3, multiclass
                                                         clus
vv                                                        AMP PEAK 24(XP21.2) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            8
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           2
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                 10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                25
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        AMP PEAK 24(XP21.2) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       0
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             20
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  48
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                               cls
clus                             0  1
  AMP PEAK 24(XP21.2) MUTATED   55 42
  AMP PEAK 24(XP21.2) WILD-TYPE 84 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.2) MUTATED     55   42
  AMP PEAK 24(XP21.2) WILD-TYPE   84   76
        clus
vv       AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE
  FEMALE                          55                            84
  MALE                            42                            76
[1] 2 2
[1] FALSE
D24V5, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.2) MUTATED    60  36
  AMP PEAK 24(XP21.2) WILD-TYPE 119  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.2) MUTATED     60   36
  AMP PEAK 24(XP21.2) WILD-TYPE  119   36
     clus
vv    AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE
  NO                           60                           119
  YES                          36                            36
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 24(XP21.2) MUTATED                             17             0
  AMP PEAK 24(XP21.2) WILD-TYPE                           42             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 24(XP21.2) MUTATED                                                                          0
  AMP PEAK 24(XP21.2) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK 24(XP21.2) MUTATED                     40
  AMP PEAK 24(XP21.2) WILD-TYPE                   63
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 24(XP21.2) MUTATED                                                  1
  AMP PEAK 24(XP21.2) WILD-TYPE                                                8
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK 24(XP21.2) MUTATED                 12
  AMP PEAK 24(XP21.2) WILD-TYPE               12
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 24(XP21.2) MUTATED                                                         13
  AMP PEAK 24(XP21.2) WILD-TYPE                                                       15
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 24(XP21.2) MUTATED                                          0
  AMP PEAK 24(XP21.2) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 24(XP21.2) MUTATED                             0
  AMP PEAK 24(XP21.2) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 24(XP21.2) MUTATED                               0
  AMP PEAK 24(XP21.2) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 24(XP21.2) MUTATED                                           14
  AMP PEAK 24(XP21.2) WILD-TYPE                                          7
D24V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 24(XP21.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      17
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              40
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   1
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        14
                                                                          clus
vv                                                                         AMP PEAK 24(XP21.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        42
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                63
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     8
  MYXOFIBROSARCOMA                                                                                    12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 24(XP21.2) MUTATED   62 26  2  7
  AMP PEAK 24(XP21.2) WILD-TYPE 90 43  7 19
D24V7, multiclass
    clus
vv   AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE
  R0                          62                            90
  R1                          26                            43
  R2                           2                             7
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(XP21.2) MUTATED       3                         7    84
  AMP PEAK 24(XP21.2) WILD-TYPE     3                        11   140
D24V8, multiclass
                           clus
vv                          AMP PEAK 24(XP21.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              84
                           clus
vv                          AMP PEAK 24(XP21.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.2) MUTATED     1  89
  AMP PEAK 24(XP21.2) WILD-TYPE   4 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.2) MUTATED      1   89
  AMP PEAK 24(XP21.2) WILD-TYPE    4  131
                        clus
vv                       AMP PEAK 24(XP21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       AMP PEAK 24(XP21.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           131
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(XQ21.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(XQ21.1) MUTATED    24  22
  AMP PEAK 25(XQ21.1) WILD-TYPE 135  76
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           46                           211 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           22                            76 
$`AMP PEAK 25(XQ21.1) MUTATED`
TCGA-DX-A6YU TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-HB-A43Z 
       34.36       106.45        13.28        22.85        30.51        37.02 
TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-PC-A5DM TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HQ 
       52.11        28.21         6.35        50.01        19.69        68.55 
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       44.91         0.56        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF 
       54.21         6.28        33.44        16.87        64.21        21.30 
TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-FX-A3TO 
       61.97        38.17        19.43        12.00        66.74        20.32 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-KD-A5QU TCGA-LI-A67I 
       19.53         3.22        37.12        13.58        35.28        30.31 
TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B 
       81.01        18.08       111.98         3.88        32.75         8.61 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X9-A973 TCGA-Z4-AAPF 
       45.34        35.18        36.43        15.95 

$`AMP PEAK 25(XQ21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       12.07       101.98        60.00        84.66        32.15        16.60 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       12.62        26.93        52.27       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       17.75         8.28        18.08        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HT 
       26.17        41.49        35.08        53.49        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A1L3 
       18.64        26.56        14.04        32.71        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       66.94        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       31.96        36.85        26.99         3.06        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       50.50        86.30       101.23        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL 
      152.12        29.49        48.20        20.05         9.34        45.14 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       47.87        40.77       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66         6.58         1.15        17.79        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       86.10         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       71.31        49.15        31.13        21.70        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
        9.80        80.48         1.38        19.89        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       63.81        16.41        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        37.55        38.63        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       46.82        48.59        35.90        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       10.52         0.72        16.77        18.94        22.82        25.35 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        84.79        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
       63.35        26.43        35.90        18.08        30.84        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        27.32         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                         0.56                          0.49 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                       111.98                        188.15 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        31.63                         31.13 
[1] "0.6 - 112.0 (31.6)" "0.5 - 188.2 (31.1)"
[1] "hr=" "1.4"
D25V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  AMP PEAK 25(XQ21.1) MUTATED                0                  2
  AMP PEAK 25(XQ21.1) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  AMP PEAK 25(XQ21.1) MUTATED                     0                   0
  AMP PEAK 25(XQ21.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  AMP PEAK 25(XQ21.1) MUTATED                               0
  AMP PEAK 25(XQ21.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  AMP PEAK 25(XQ21.1) MUTATED                       0                      5
  AMP PEAK 25(XQ21.1) WILD-TYPE                     1                     23
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  AMP PEAK 25(XQ21.1) MUTATED                      0                    0
  AMP PEAK 25(XQ21.1) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  AMP PEAK 25(XQ21.1) MUTATED                                       0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  AMP PEAK 25(XQ21.1) MUTATED                                  0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  AMP PEAK 25(XQ21.1) MUTATED                                                0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  AMP PEAK 25(XQ21.1) MUTATED                                 2
  AMP PEAK 25(XQ21.1) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  AMP PEAK 25(XQ21.1) MUTATED                                         0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  AMP PEAK 25(XQ21.1) MUTATED                              0
  AMP PEAK 25(XQ21.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  AMP PEAK 25(XQ21.1) MUTATED                         0
  AMP PEAK 25(XQ21.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  AMP PEAK 25(XQ21.1) MUTATED                                  4
  AMP PEAK 25(XQ21.1) WILD-TYPE                               13
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  AMP PEAK 25(XQ21.1) MUTATED                                         1
  AMP PEAK 25(XQ21.1) WILD-TYPE                                       4
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  AMP PEAK 25(XQ21.1) MUTATED                             12
  AMP PEAK 25(XQ21.1) WILD-TYPE                           32
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  AMP PEAK 25(XQ21.1) MUTATED                                         0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  AMP PEAK 25(XQ21.1) MUTATED                                           0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  AMP PEAK 25(XQ21.1) MUTATED                                                  0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  AMP PEAK 25(XQ21.1) MUTATED                                          1
  AMP PEAK 25(XQ21.1) WILD-TYPE                                        7
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  AMP PEAK 25(XQ21.1) MUTATED                                                         0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  AMP PEAK 25(XQ21.1) MUTATED                                            0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  AMP PEAK 25(XQ21.1) MUTATED                                                  17
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                56
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  AMP PEAK 25(XQ21.1) MUTATED                                                    0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  AMP PEAK 25(XQ21.1) MUTATED                                    0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  AMP PEAK 25(XQ21.1) MUTATED                          0
  AMP PEAK 25(XQ21.1) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  AMP PEAK 25(XQ21.1) MUTATED                             0
  AMP PEAK 25(XQ21.1) WILD-TYPE                           4
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  AMP PEAK 25(XQ21.1) MUTATED                           0
  AMP PEAK 25(XQ21.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  AMP PEAK 25(XQ21.1) MUTATED                                   0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                 7
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  AMP PEAK 25(XQ21.1) MUTATED                                   2
  AMP PEAK 25(XQ21.1) WILD-TYPE                                 3
D25V3, multiclass
                                                         clus
vv                                                        AMP PEAK 25(XQ21.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            5
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           1
  LOWER EXTREMITY - THIGH/KNEE                                                     12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       0
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        AMP PEAK 25(XQ21.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             23
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             4
  LOWER EXTREMITY - THIGH/KNEE                                                       32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         4
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED    28  18
  AMP PEAK 25(XQ21.1) WILD-TYPE 111 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED     28   18
  AMP PEAK 25(XQ21.1) WILD-TYPE  111  100
        clus
vv       AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  FEMALE                          28                           111
  MALE                            18                           100
[1] 2 2
[1] FALSE
D25V5, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED    28  16
  AMP PEAK 25(XQ21.1) WILD-TYPE 151  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED     28   16
  AMP PEAK 25(XQ21.1) WILD-TYPE  151   56
     clus
vv    AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  NO                           28                           151
  YES                          16                            56
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  AMP PEAK 25(XQ21.1) MUTATED                             15             0
  AMP PEAK 25(XQ21.1) WILD-TYPE                           44             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  AMP PEAK 25(XQ21.1) MUTATED                                                                          0
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  AMP PEAK 25(XQ21.1) MUTATED                     12
  AMP PEAK 25(XQ21.1) WILD-TYPE                   91
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  AMP PEAK 25(XQ21.1) MUTATED                                                  1
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                8
                               vv
clus                            MYXOFIBROSARCOMA
  AMP PEAK 25(XQ21.1) MUTATED                  5
  AMP PEAK 25(XQ21.1) WILD-TYPE               19
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  AMP PEAK 25(XQ21.1) MUTATED                                                          7
  AMP PEAK 25(XQ21.1) WILD-TYPE                                                       21
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  AMP PEAK 25(XQ21.1) MUTATED                                          1
  AMP PEAK 25(XQ21.1) WILD-TYPE                                        1
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  AMP PEAK 25(XQ21.1) MUTATED                             0
  AMP PEAK 25(XQ21.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  AMP PEAK 25(XQ21.1) MUTATED                               0
  AMP PEAK 25(XQ21.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  AMP PEAK 25(XQ21.1) MUTATED                                            5
  AMP PEAK 25(XQ21.1) WILD-TYPE                                         16
D25V6, multiclass
                                                                          clus
vv                                                                         AMP PEAK 25(XQ21.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      15
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   1
  MYXOFIBROSARCOMA                                                                                   5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         5
                                                                          clus
vv                                                                         AMP PEAK 25(XQ21.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        44
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                91
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     8
  MYXOFIBROSARCOMA                                                                                    19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 25(XQ21.1) MUTATED    26  14   2   4
  AMP PEAK 25(XQ21.1) WILD-TYPE 126  55   7  22
D25V7, multiclass
    clus
vv   AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  R0                          26                           126
  R1                          14                            55
  R2                           2                             7
  RX                           4                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(XQ21.1) MUTATED       0                         1    42
  AMP PEAK 25(XQ21.1) WILD-TYPE     6                        17   182
D25V8, multiclass
                           clus
vv                          AMP PEAK 25(XQ21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              42
                           clus
vv                          AMP PEAK 25(XQ21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED     2  39
  AMP PEAK 25(XQ21.1) WILD-TYPE   3 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED      2   39
  AMP PEAK 25(XQ21.1) WILD-TYPE    3  181
                        clus
vv                       AMP PEAK 25(XQ21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       AMP PEAK 25(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           181
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED    45  24
  DEL PEAK  1(1P36.32) WILD-TYPE 114  74
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            69                            188 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            24                             74 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-AB2W TCGA-DX-AB2X TCGA-HB-A43Z 
       67.20        34.36        75.32       106.45        13.28        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-QQ-A8VB 
       12.62        26.93        52.27       159.29        22.62       188.15 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HQ TCGA-3B-A9HR 
       26.17        41.49        35.08        50.01        68.55        88.57 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A3LW TCGA-DX-A3U5 
       25.25        14.37        26.56        68.61       136.44        31.86 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J 
       51.02        14.99        10.68        68.55        85.45         9.73 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A8BJ 
       82.68        36.33       101.23        21.30        30.35         9.34 
TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A48G TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EK 
      106.55        21.70        19.89         0.72         9.80         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-K1-A42W TCGA-K1-A42X 
       37.12       171.09        13.58        85.97        62.17       123.78 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DK 
       63.81        16.41        35.28        14.99        10.45       122.96 
TCGA-PC-A5DL TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       37.55        32.75        19.63        84.79        38.27        65.46 
TCGA-WP-A9GB TCGA-X6-A7WD TCGA-X6-A8C5 
        8.58        30.84        50.86 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        34.68        16.18        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 
       14.43        14.07        15.85        40.60        12.07        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       52.11        28.21        11.70        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS 
       18.08        20.94        17.52        19.69        53.49        44.91 
TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       54.74        42.84        10.32        38.47        36.03        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        32.71        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD 
       33.44        44.68        35.77         4.54        73.87        50.43 
TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6B9 
       34.88        45.99        24.26        35.28        15.95        37.41 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       78.28        50.50        16.87        86.30        64.21        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       62.20       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       40.44        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       31.13        20.32        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
        4.57        33.30        80.48        19.53         3.22        19.89 
TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       25.22         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y8 
       53.33        17.36        23.38         5.19        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        21.73        19.73        17.98        22.39        11.57 
TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        7.36        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        22.82        25.35         8.61        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8Y0 TCGA-X2-A95T 
       10.72        12.46        11.93         4.80        22.62        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 
       26.43        35.90        18.08        45.34        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        188.15                         152.12 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         37.12                          27.88 
[1] "0.7 - 188.2 (37.1)" "0.5 - 152.1 (27.9)"
[1] "hr=" "1.6"
D26V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  1(1P36.32) MUTATED                0                  3
  DEL PEAK  1(1P36.32) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  1(1P36.32) MUTATED                     0                   0
  DEL PEAK  1(1P36.32) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  1(1P36.32) MUTATED                               0
  DEL PEAK  1(1P36.32) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  1(1P36.32) MUTATED                       1                     16
  DEL PEAK  1(1P36.32) WILD-TYPE                     0                     12
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  1(1P36.32) MUTATED                      0                    0
  DEL PEAK  1(1P36.32) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  1(1P36.32) MUTATED                                       0
  DEL PEAK  1(1P36.32) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  1(1P36.32) MUTATED                                  0
  DEL PEAK  1(1P36.32) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  1(1P36.32) MUTATED                                                2
  DEL PEAK  1(1P36.32) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  1(1P36.32) MUTATED                                 3
  DEL PEAK  1(1P36.32) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  1(1P36.32) MUTATED                                         0
  DEL PEAK  1(1P36.32) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  1(1P36.32) MUTATED                              1
  DEL PEAK  1(1P36.32) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK  1(1P36.32) MUTATED                         0
  DEL PEAK  1(1P36.32) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  1(1P36.32) MUTATED                                  3
  DEL PEAK  1(1P36.32) WILD-TYPE                               14
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  1(1P36.32) MUTATED                                         0
  DEL PEAK  1(1P36.32) WILD-TYPE                                       5
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  1(1P36.32) MUTATED                              8
  DEL PEAK  1(1P36.32) WILD-TYPE                           36
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  1(1P36.32) MUTATED                                         1
  DEL PEAK  1(1P36.32) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  1(1P36.32) MUTATED                                           1
  DEL PEAK  1(1P36.32) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  1(1P36.32) MUTATED                                                  1
  DEL PEAK  1(1P36.32) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  1(1P36.32) MUTATED                                          3
  DEL PEAK  1(1P36.32) WILD-TYPE                                        5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  1(1P36.32) MUTATED                                                         1
  DEL PEAK  1(1P36.32) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  1(1P36.32) MUTATED                                            1
  DEL PEAK  1(1P36.32) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  1(1P36.32) MUTATED                                                  19
  DEL PEAK  1(1P36.32) WILD-TYPE                                                54
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  1(1P36.32) MUTATED                                                    2
  DEL PEAK  1(1P36.32) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  1(1P36.32) MUTATED                                    0
  DEL PEAK  1(1P36.32) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK  1(1P36.32) MUTATED                          1
  DEL PEAK  1(1P36.32) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  1(1P36.32) MUTATED                             1
  DEL PEAK  1(1P36.32) WILD-TYPE                           3
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK  1(1P36.32) MUTATED                           0
  DEL PEAK  1(1P36.32) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  1(1P36.32) MUTATED                                   0
  DEL PEAK  1(1P36.32) WILD-TYPE                                 7
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  1(1P36.32) MUTATED                                   1
  DEL PEAK  1(1P36.32) WILD-TYPE                                 4
D26V3, multiclass
                                                         clus
vv                                                        DEL PEAK  1(1P36.32) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            16
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            0
  LOWER EXTREMITY - THIGH/KNEE                                                       8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 19
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        1
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        DEL PEAK  1(1P36.32) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              12
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              5
  LOWER EXTREMITY - THIGH/KNEE                                                        36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   54
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          3
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED   50 19
  DEL PEAK  1(1P36.32) WILD-TYPE 89 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     50   19
  DEL PEAK  1(1P36.32) WILD-TYPE   89   99
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           50                             89
  MALE                             19                             99
[1] 2 2
[1] FALSE
D26V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    56  11
  DEL PEAK  1(1P36.32) WILD-TYPE 123  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     56   11
  DEL PEAK  1(1P36.32) WILD-TYPE  123   61
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                            56                            123
  YES                           11                             61
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  1(1P36.32) MUTATED                              5             0
  DEL PEAK  1(1P36.32) WILD-TYPE                           54             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  1(1P36.32) MUTATED                                                                          0
  DEL PEAK  1(1P36.32) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK  1(1P36.32) MUTATED                     51
  DEL PEAK  1(1P36.32) WILD-TYPE                   52
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  1(1P36.32) MUTATED                                                  3
  DEL PEAK  1(1P36.32) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK  1(1P36.32) MUTATED                  4
  DEL PEAK  1(1P36.32) WILD-TYPE               20
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  1(1P36.32) MUTATED                                                          4
  DEL PEAK  1(1P36.32) WILD-TYPE                                                       24
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  1(1P36.32) MUTATED                                          0
  DEL PEAK  1(1P36.32) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  1(1P36.32) MUTATED                             0
  DEL PEAK  1(1P36.32) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  1(1P36.32) MUTATED                               1
  DEL PEAK  1(1P36.32) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  1(1P36.32) MUTATED                                            1
  DEL PEAK  1(1P36.32) WILD-TYPE                                         20
D26V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  1(1P36.32) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        5
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               51
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                    4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          1
                                                                          clus
vv                                                                         DEL PEAK  1(1P36.32) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         54
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 52
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             24
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.32) MUTATED    48  12   1   8
  DEL PEAK  1(1P36.32) WILD-TYPE 104  57   8  18
D26V7, multiclass
    clus
vv   DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  R0                           48                            104
  R1                           12                             57
  R2                            1                              8
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       2                         6    58
  DEL PEAK  1(1P36.32) WILD-TYPE     4                        12   166
D26V8, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               58
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     0  60
  DEL PEAK  1(1P36.32) WILD-TYPE   5 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      0   60
  DEL PEAK  1(1P36.32) WILD-TYPE    5  160
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            160
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  2(1Q44) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1Q44) MUTATED    45  35
  DEL PEAK  2(1Q44) WILD-TYPE 114  63
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         80                         177 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         35                          63 
$`DEL PEAK  2(1Q44) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2P 
       31.53        34.68        67.20        17.95        14.43        12.07 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-KF-A41W TCGA-LI-A9QH 
       13.28        30.51        32.15        12.62        11.70        17.75 
TCGA-PC-A5DP TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-DX-A1KX 
       18.08        17.52        35.08        50.01        19.69        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A3LW 
       12.85        45.11        18.54        54.21        85.02       136.44 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A48J TCGA-DX-A6B8 TCGA-DX-A6BA 
       33.44        31.86        51.02         9.73        15.95        82.68 
TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6Z0 TCGA-DX-A7EF 
       31.96         3.06        41.00        78.28        64.21        21.30 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
        9.34        61.97        40.77       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS 
       36.69        66.74        77.88       106.55        50.40        49.15 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA 
       20.32        19.89        67.63         4.57        33.30         9.80 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-KD-A5QS TCGA-MB-A5Y8 
        3.22        19.89        37.12        13.58        63.81        25.41 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-RN-AAAQ 
       21.73         7.36        81.01        17.65        48.59        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7W8 TCGA-X6-A7WD 
       10.72        12.46        38.27        65.46        26.43        30.84 
TCGA-X6-A8C2 TCGA-Z4-AAPG 
       35.18        15.98 

$`DEL PEAK  2(1Q44) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BP 
       36.30        16.18        34.36        75.32        15.22        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       15.85        40.60       106.45        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       84.66        16.60        37.02        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX 
       28.21       159.29        22.62         8.28         6.35        20.94 
TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
      188.15        26.17        41.49        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       32.71        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M1 
       95.38        79.17         9.04        49.05        86.83        44.68 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       50.43        34.88        85.45        45.99        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV 
       37.41        36.33        28.96        36.85        26.99        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       16.87        86.30       101.23        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BL TCGA-DX-A8BM 
      152.12        29.49        48.20        20.05        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       38.17        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB3B 
       12.00        15.72        65.98        86.10         9.21        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       71.31        31.13        21.70        15.48         8.05        34.88 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 
        0.72        80.48        19.53         1.38        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       16.41        35.28        30.31         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57        10.45       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        13.08         1.84        46.82        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       19.63        13.22        13.41        11.93         4.80        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                       3.06                        0.49 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                     150.35                      188.15 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                     30.675                      32.710 
[1] "3.1 - 150.3 (30.7)" "0.5 - 188.2 (32.7)"
[1] "hr=" "1.3"
D27V2, continuous
                             vv
clus                          CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  2(1Q44) MUTATED                0                  3
  DEL PEAK  2(1Q44) WILD-TYPE              1                  4
                             vv
clus                          CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  2(1Q44) MUTATED                     0                   0
  DEL PEAK  2(1Q44) WILD-TYPE                   2                   1
                             vv
clus                          CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  2(1Q44) MUTATED                               0
  DEL PEAK  2(1Q44) WILD-TYPE                             2
                             vv
clus                          GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  2(1Q44) MUTATED                       0                      6
  DEL PEAK  2(1Q44) WILD-TYPE                     1                     22
                             vv
clus                          HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  2(1Q44) MUTATED                      0                    0
  DEL PEAK  2(1Q44) WILD-TYPE                    2                    1
                             vv
clus                          HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  2(1Q44) MUTATED                                       0
  DEL PEAK  2(1Q44) WILD-TYPE                                     2
                             vv
clus                          LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  2(1Q44) MUTATED                                  0
  DEL PEAK  2(1Q44) WILD-TYPE                                1
                             vv
clus                          LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  2(1Q44) MUTATED                                                0
  DEL PEAK  2(1Q44) WILD-TYPE                                              2
                             vv
clus                          LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  2(1Q44) MUTATED                                 2
  DEL PEAK  2(1Q44) WILD-TYPE                               8
                             vv
clus                          LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  2(1Q44) MUTATED                                         0
  DEL PEAK  2(1Q44) WILD-TYPE                                       2
                             vv
clus                          LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  2(1Q44) MUTATED                              0
  DEL PEAK  2(1Q44) WILD-TYPE                            4
                             vv
clus                          LOWER EXTREMITY - GROIN
  DEL PEAK  2(1Q44) MUTATED                         1
  DEL PEAK  2(1Q44) WILD-TYPE                       1
                             vv
clus                          LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  2(1Q44) MUTATED                                  7
  DEL PEAK  2(1Q44) WILD-TYPE                               10
                             vv
clus                          LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  2(1Q44) MUTATED                                         4
  DEL PEAK  2(1Q44) WILD-TYPE                                       1
                             vv
clus                          LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  2(1Q44) MUTATED                             19
  DEL PEAK  2(1Q44) WILD-TYPE                           25
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  2(1Q44) MUTATED                                         0
  DEL PEAK  2(1Q44) WILD-TYPE                                       4
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  2(1Q44) MUTATED                                           0
  DEL PEAK  2(1Q44) WILD-TYPE                                         2
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  2(1Q44) MUTATED                                                  1
  DEL PEAK  2(1Q44) WILD-TYPE                                                4
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  2(1Q44) MUTATED                                          3
  DEL PEAK  2(1Q44) WILD-TYPE                                        5
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  2(1Q44) MUTATED                                                         1
  DEL PEAK  2(1Q44) WILD-TYPE                                                       1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  2(1Q44) MUTATED                                            0
  DEL PEAK  2(1Q44) WILD-TYPE                                          1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  2(1Q44) MUTATED                                                  21
  DEL PEAK  2(1Q44) WILD-TYPE                                                52
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  2(1Q44) MUTATED                                                    1
  DEL PEAK  2(1Q44) WILD-TYPE                                                  2
                             vv
clus                          SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  2(1Q44) MUTATED                                    1
  DEL PEAK  2(1Q44) WILD-TYPE                                  1
                             vv
clus                          SUPERFICIAL TRUNK - BACK
  DEL PEAK  2(1Q44) MUTATED                          1
  DEL PEAK  2(1Q44) WILD-TYPE                        4
                             vv
clus                          SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  2(1Q44) MUTATED                             2
  DEL PEAK  2(1Q44) WILD-TYPE                           2
                             vv
clus                          SUPERFICIAL TRUNK - FLANK
  DEL PEAK  2(1Q44) MUTATED                           0
  DEL PEAK  2(1Q44) WILD-TYPE                         1
                             vv
clus                          UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  2(1Q44) MUTATED                                   3
  DEL PEAK  2(1Q44) WILD-TYPE                                 4
                             vv
clus                          UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  2(1Q44) MUTATED                                   3
  DEL PEAK  2(1Q44) WILD-TYPE                                 2
D27V3, multiclass
                                                         clus
vv                                                        DEL PEAK  2(1Q44) MUTATED
  CHEST - BREAST                                                                  0
  CHEST - CHEST WALL                                                              3
  CHEST - LUNG/PLEURA                                                             0
  CHEST - MEDIASTINUM                                                             0
  CHEST - OTHER (PLEASE SPECIFY                                                   0
  GYNECOLOGICAL - OVARY                                                           0
  GYNECOLOGICAL - UTERUS                                                          6
  HEAD AND NECK - HEAD                                                            0
  HEAD AND NECK - NECK                                                            0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                           0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                 2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                         0
  LOWER EXTREMITY - FOOT/ANKLE                                                    0
  LOWER EXTREMITY - GROIN                                                         1
  LOWER EXTREMITY - LOWER LEG/CALF                                                7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                         4
  LOWER EXTREMITY - THIGH/KNEE                                                   19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                        3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                         1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                      0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                              21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                              1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                              1
  SUPERFICIAL TRUNK - BACK                                                        1
  SUPERFICIAL TRUNK - BUTTOCK                                                     2
  SUPERFICIAL TRUNK - FLANK                                                       0
  UPPER EXTREMITY - SHOULDER/AXILLA                                               3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                               3
                                                         clus
vv                                                        DEL PEAK  2(1Q44) WILD-TYPE
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                4
  CHEST - LUNG/PLEURA                                                               2
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           22
  HEAD AND NECK - HEAD                                                              2
  HEAD AND NECK - NECK                                                              1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           2
  LOWER EXTREMITY - FOOT/ANKLE                                                      4
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           1
  LOWER EXTREMITY - THIGH/KNEE                                                     25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                52
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          4
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q44) MUTATED   42 38
  DEL PEAK  2(1Q44) WILD-TYPE 97 80
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED     42   38
  DEL PEAK  2(1Q44) WILD-TYPE   97   80
        clus
vv       DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  FEMALE                        42                          97
  MALE                          38                          80
[1] 2 2
[1] FALSE
D27V5, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q44) MUTATED    45  34
  DEL PEAK  2(1Q44) WILD-TYPE 134  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED     45   34
  DEL PEAK  2(1Q44) WILD-TYPE  134   38
     clus
vv    DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  NO                         45                         134
  YES                        34                          38
[1] 2 2
[1] FALSE
                             vv
clus                          DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  2(1Q44) MUTATED                             19             0
  DEL PEAK  2(1Q44) WILD-TYPE                           40             2
                             vv
clus                          GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  2(1Q44) MUTATED                                                                          0
  DEL PEAK  2(1Q44) WILD-TYPE                                                                        1
                             vv
clus                          LEIOMYOSARCOMA (LMS)
  DEL PEAK  2(1Q44) MUTATED                     18
  DEL PEAK  2(1Q44) WILD-TYPE                   85
                             vv
clus                          MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  2(1Q44) MUTATED                                                  4
  DEL PEAK  2(1Q44) WILD-TYPE                                                5
                             vv
clus                          MYXOFIBROSARCOMA
  DEL PEAK  2(1Q44) MUTATED                 10
  DEL PEAK  2(1Q44) WILD-TYPE               14
                             vv
clus                          PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  2(1Q44) MUTATED                                                         16
  DEL PEAK  2(1Q44) WILD-TYPE                                                       12
                             vv
clus                          SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  2(1Q44) MUTATED                                          0
  DEL PEAK  2(1Q44) WILD-TYPE                                        2
                             vv
clus                          SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  2(1Q44) MUTATED                             0
  DEL PEAK  2(1Q44) WILD-TYPE                           2
                             vv
clus                          SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  2(1Q44) MUTATED                               0
  DEL PEAK  2(1Q44) WILD-TYPE                             6
                             vv
clus                          UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  2(1Q44) MUTATED                                           13
  DEL PEAK  2(1Q44) WILD-TYPE                                          8
D27V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  2(1Q44) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                    19
  DESMOID TUMOR                                                                                    0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                         0
  LEIOMYOSARCOMA (LMS)                                                                            18
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                 4
  MYXOFIBROSARCOMA                                                                                10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                        16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                         0
  SYNOVIAL SARCOMA - BIPHASIC                                                                      0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                    0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                      13
                                                                          clus
vv                                                                         DEL PEAK  2(1Q44) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                      40
  DESMOID TUMOR                                                                                      2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           1
  LEIOMYOSARCOMA (LMS)                                                                              85
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   5
  MYXOFIBROSARCOMA                                                                                  14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           2
  SYNOVIAL SARCOMA - BIPHASIC                                                                        2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1Q44) MUTATED    41  27   1  10
  DEL PEAK  2(1Q44) WILD-TYPE 111  42   8  16
D27V7, multiclass
    clus
vv   DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  R0                        41                         111
  R1                        27                          42
  R2                         1                           8
  RX                        10                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q44) MUTATED       0                         7    70
  DEL PEAK  2(1Q44) WILD-TYPE     6                        11   154
D27V8, multiclass
                           clus
vv                          DEL PEAK  2(1Q44) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            70
                           clus
vv                          DEL PEAK  2(1Q44) WILD-TYPE
  ASIAN                                               6
  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"
D27V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q44) MUTATED     1  72
  DEL PEAK  2(1Q44) WILD-TYPE   4 148
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED      1   72
  DEL PEAK  2(1Q44) WILD-TYPE    4  148
                        clus
vv                       DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        72                         148
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    53  41
  DEL PEAK  3(2P25.3) WILD-TYPE 106  57
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           94                           163 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           41                            57 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       34.68        67.20        34.36        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z 
       12.07       106.45        30.51        84.66        32.15        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-PC-A5DP 
       12.62        52.11        52.27        22.62        17.75        18.08 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY 
       35.08        19.69        88.57        44.91        25.25        10.32 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1L2 TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 
       18.64        26.56        85.02        33.44        44.68        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O 
       68.55        50.43        34.88        85.45        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BF 
       46.03        59.84        15.95        37.41        82.68        31.96 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM 
        3.06        41.00        78.28        16.87        21.30        62.20 
TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU 
       30.35        61.97        47.87        40.77        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       60.66         6.58        12.00        77.88       106.55        50.40 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EJ 
       19.89        67.63        34.88        33.30         0.72         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN 
       19.89        25.22        13.58        85.97        16.41       101.26 
TCGA-K1-A42W TCGA-KD-A5QU TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-AA9N 
       62.17        35.28        14.99         7.36        81.01        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B 
       46.82        10.52        16.77        18.94        22.82         8.61 
TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 
       12.46        84.79        38.27        65.46         8.58        26.43 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X9-A971 
       18.08        30.84        35.18        27.32 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        16.18        75.32        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-FX-A3NK 
       40.60        13.28        22.85       101.98        60.00        16.60 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM 
       26.93        28.21       159.29        11.70         8.28         6.35 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI 
       20.94       188.15        17.52        26.17        41.49        50.01 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ 
       53.49        68.55        54.74        14.37        42.84        38.47 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       36.03         0.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        18.54        54.21        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       86.83       136.44        31.86        35.77        51.02         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48R 
       10.68        73.87         9.73        45.99        35.28        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
      108.82        37.58        36.33        28.96        36.85        26.99 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EO 
       50.50        86.30        64.21       101.23        34.49       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN 
       29.49        48.20        20.05         9.34        45.14        38.17 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
      150.35        40.44        19.43         1.15        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        86.10        66.74         9.21        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        20.32        15.48         8.05 
TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
        4.57         9.80        80.48        19.53         1.38        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
      171.09         5.92         1.05         3.91        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
       17.36        23.38         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       25.41         0.49        21.73        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 
       11.57        10.45       122.96        37.55        38.63        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
      111.98        64.77         0.72         3.88        25.35        32.75 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        10.72        11.93         4.80 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.62        63.35        35.90        45.34        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       50.86        29.46        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.72                          0.49 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       106.55                        188.15 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       32.725                        29.490 
[1] "0.7 - 106.5 (32.7)" "0.5 - 188.2 (29.5)"
[1] "hr=" "1.2"
D28V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  3(2P25.3) MUTATED                0                  2
  DEL PEAK  3(2P25.3) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  3(2P25.3) MUTATED                     0                   0
  DEL PEAK  3(2P25.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  3(2P25.3) MUTATED                               1
  DEL PEAK  3(2P25.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  3(2P25.3) MUTATED                       0                     14
  DEL PEAK  3(2P25.3) WILD-TYPE                     1                     14
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  3(2P25.3) MUTATED                      0                    0
  DEL PEAK  3(2P25.3) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  3(2P25.3) MUTATED                                       0
  DEL PEAK  3(2P25.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  3(2P25.3) MUTATED                                  0
  DEL PEAK  3(2P25.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  3(2P25.3) MUTATED                                                2
  DEL PEAK  3(2P25.3) WILD-TYPE                                              0
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  3(2P25.3) MUTATED                                 2
  DEL PEAK  3(2P25.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  3(2P25.3) MUTATED                                         0
  DEL PEAK  3(2P25.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  3(2P25.3) MUTATED                              0
  DEL PEAK  3(2P25.3) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK  3(2P25.3) MUTATED                         0
  DEL PEAK  3(2P25.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  3(2P25.3) MUTATED                                  6
  DEL PEAK  3(2P25.3) WILD-TYPE                               11
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  3(2P25.3) MUTATED                                         3
  DEL PEAK  3(2P25.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  3(2P25.3) MUTATED                             22
  DEL PEAK  3(2P25.3) WILD-TYPE                           22
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  3(2P25.3) MUTATED                                         1
  DEL PEAK  3(2P25.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  3(2P25.3) MUTATED                                           1
  DEL PEAK  3(2P25.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  3(2P25.3) MUTATED                                                  0
  DEL PEAK  3(2P25.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  3(2P25.3) MUTATED                                          2
  DEL PEAK  3(2P25.3) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  3(2P25.3) MUTATED                                                         0
  DEL PEAK  3(2P25.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  3(2P25.3) MUTATED                                            1
  DEL PEAK  3(2P25.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  3(2P25.3) MUTATED                                                  25
  DEL PEAK  3(2P25.3) WILD-TYPE                                                48
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  3(2P25.3) MUTATED                                                    1
  DEL PEAK  3(2P25.3) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  3(2P25.3) MUTATED                                    2
  DEL PEAK  3(2P25.3) WILD-TYPE                                  0
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK  3(2P25.3) MUTATED                          2
  DEL PEAK  3(2P25.3) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  3(2P25.3) MUTATED                             3
  DEL PEAK  3(2P25.3) WILD-TYPE                           1
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK  3(2P25.3) MUTATED                           0
  DEL PEAK  3(2P25.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  3(2P25.3) MUTATED                                   3
  DEL PEAK  3(2P25.3) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  3(2P25.3) MUTATED                                   1
  DEL PEAK  3(2P25.3) WILD-TYPE                                 4
D28V3, multiclass
                                                         clus
vv                                                        DEL PEAK  3(2P25.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           14
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                25
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       3
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 1
                                                         clus
vv                                                        DEL PEAK  3(2P25.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             14
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  48
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  0
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         1
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(2P25.3) MUTATED   60 34
  DEL PEAK  3(2P25.3) WILD-TYPE 79 84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     60   34
  DEL PEAK  3(2P25.3) WILD-TYPE   79   84
        clus
vv       DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  FEMALE                          60                            79
  MALE                            34                            84
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    62  31
  DEL PEAK  3(2P25.3) WILD-TYPE 117  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     62   31
  DEL PEAK  3(2P25.3) WILD-TYPE  117   41
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                           62                           117
  YES                          31                            41
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  3(2P25.3) MUTATED                             10             0
  DEL PEAK  3(2P25.3) WILD-TYPE                           49             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  3(2P25.3) MUTATED                                                                          0
  DEL PEAK  3(2P25.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK  3(2P25.3) MUTATED                     48
  DEL PEAK  3(2P25.3) WILD-TYPE                   55
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  3(2P25.3) MUTATED                                                  3
  DEL PEAK  3(2P25.3) WILD-TYPE                                                6
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK  3(2P25.3) MUTATED                 12
  DEL PEAK  3(2P25.3) WILD-TYPE               12
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  3(2P25.3) MUTATED                                                         13
  DEL PEAK  3(2P25.3) WILD-TYPE                                                       15
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  3(2P25.3) MUTATED                                          0
  DEL PEAK  3(2P25.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  3(2P25.3) MUTATED                             0
  DEL PEAK  3(2P25.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  3(2P25.3) MUTATED                               0
  DEL PEAK  3(2P25.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  3(2P25.3) MUTATED                                            8
  DEL PEAK  3(2P25.3) WILD-TYPE                                         13
D28V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  3(2P25.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      10
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              48
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   3
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
                                                                          clus
vv                                                                         DEL PEAK  3(2P25.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        49
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                55
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     6
  MYXOFIBROSARCOMA                                                                                    12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(2P25.3) MUTATED   65 18  3  7
  DEL PEAK  3(2P25.3) WILD-TYPE 87 51  6 19
D28V7, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          65                            87
  R1                          18                            51
  R2                           3                             6
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P25.3) MUTATED       1                        13    75
  DEL PEAK  3(2P25.3) WILD-TYPE     5                         5   149
D28V8, multiclass
                           clus
vv                          DEL PEAK  3(2P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                              75
                           clus
vv                          DEL PEAK  3(2P25.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     0  87
  DEL PEAK  3(2P25.3) WILD-TYPE   5 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      0   87
  DEL PEAK  3(2P25.3) WILD-TYPE    5  133
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           133
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    57  51
  DEL PEAK  4(2Q37.3) WILD-TYPE 102  47
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          108                           149 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           51                            47 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       34.68        16.18        67.20        34.36        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A 
       14.43        15.85        12.07       101.98        30.51        32.15 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM 
       52.11        26.93        28.21        22.62        11.70         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR 
       18.08        20.94        17.52        50.01        19.69        88.57 
TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KY 
       44.91        14.37        42.84        18.64        26.56        12.85 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M1 TCGA-DX-A3U5 
       18.54        54.21        85.02         6.28        44.68        31.86 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L 
       51.02        14.99        10.68        50.43        85.45        24.26 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       26.47        59.84        15.95        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN 
       78.28        50.50        16.87        21.30        62.20        30.35 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS 
        9.34        61.97        45.14        47.87        38.17        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T 
       40.44        36.69        60.66        86.10        66.74        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
      106.55        50.40        19.89        67.63        34.88         4.57 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA 
        9.80        80.48         3.22        19.89        37.12        13.58 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV 
       16.41         1.05        53.33        62.17        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-A7B5 
       63.81        16.41        35.28         7.36        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B 
       17.65        10.52        18.94         3.88        22.82         8.61 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB 
       10.72        12.46        84.79        38.27        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        18.08        30.84        35.18        19.17 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2W 
       36.30        31.53        75.32        14.07        40.60       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z 
       13.28        22.85        60.00        84.66        16.60        37.02 
TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QQ-A8VB 
       12.62        52.27       159.29        17.75         8.28       188.15 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT 
       26.17        41.49        35.08        53.49        68.55        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       25.25        10.32        38.47        36.03         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       32.71        68.61        45.11        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
      136.44        33.44        35.77         4.54        73.87        68.55 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        45.99        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
      108.82        37.58        37.41        82.68        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       36.85        26.99        86.30        64.21       101.23        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BO TCGA-DX-A8BR 
      152.12        29.49        48.20        20.05        40.77       150.35 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       65.98         9.21        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HS-A5N7 TCGA-HS-A5N8 
       21.70        20.32        15.48         8.05        33.30         0.72 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.53         1.38        25.22       171.09        85.97         5.92 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-MB-A5Y8 
        3.91       101.26       123.78        17.36        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 
       11.57        10.45       122.96        37.55        38.63         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
      111.98        64.77         0.72        16.77        25.35        32.75 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY 
       19.63        13.22        13.41        11.93         4.80        65.46 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       35.90        45.34        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         1.05                          0.49 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       106.55                        188.15 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       26.745                        33.530 
[1] "1.1 - 106.5 (26.7)" "0.5 - 188.2 (33.5)"
[1] "hr=" "1.7"
D29V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  4(2Q37.3) MUTATED                0                  5
  DEL PEAK  4(2Q37.3) WILD-TYPE              1                  2
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  4(2Q37.3) MUTATED                     0                   0
  DEL PEAK  4(2Q37.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                               1
  DEL PEAK  4(2Q37.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  4(2Q37.3) MUTATED                       0                     18
  DEL PEAK  4(2Q37.3) WILD-TYPE                     1                     10
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  4(2Q37.3) MUTATED                      1                    0
  DEL PEAK  4(2Q37.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                                       0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  4(2Q37.3) MUTATED                                  1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                0
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                                                1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  4(2Q37.3) MUTATED                                 2
  DEL PEAK  4(2Q37.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  4(2Q37.3) MUTATED                                         0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  4(2Q37.3) MUTATED                              1
  DEL PEAK  4(2Q37.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK  4(2Q37.3) MUTATED                         0
  DEL PEAK  4(2Q37.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  4(2Q37.3) MUTATED                                  6
  DEL PEAK  4(2Q37.3) WILD-TYPE                               11
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                                         5
  DEL PEAK  4(2Q37.3) WILD-TYPE                                       0
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  4(2Q37.3) MUTATED                             23
  DEL PEAK  4(2Q37.3) WILD-TYPE                           21
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  4(2Q37.3) MUTATED                                         1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  4(2Q37.3) MUTATED                                           1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  4(2Q37.3) MUTATED                                                  0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  4(2Q37.3) MUTATED                                          3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  4(2Q37.3) MUTATED                                                         0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  4(2Q37.3) MUTATED                                            1
  DEL PEAK  4(2Q37.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  4(2Q37.3) MUTATED                                                  26
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                47
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  4(2Q37.3) MUTATED                                                    0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  4(2Q37.3) MUTATED                                    2
  DEL PEAK  4(2Q37.3) WILD-TYPE                                  0
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK  4(2Q37.3) MUTATED                          2
  DEL PEAK  4(2Q37.3) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  4(2Q37.3) MUTATED                             2
  DEL PEAK  4(2Q37.3) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK  4(2Q37.3) MUTATED                           0
  DEL PEAK  4(2Q37.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  4(2Q37.3) MUTATED                                   3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  4(2Q37.3) MUTATED                                   3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                 2
D29V3, multiclass
                                                         clus
vv                                                        DEL PEAK  4(2Q37.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                5
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           18
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           5
  LOWER EXTREMITY - THIGH/KNEE                                                     23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                26
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        DEL PEAK  4(2Q37.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             10
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             0
  LOWER EXTREMITY - THIGH/KNEE                                                       21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  47
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  0
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   59 49
  DEL PEAK  4(2Q37.3) WILD-TYPE 80 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     59   49
  DEL PEAK  4(2Q37.3) WILD-TYPE   80   69
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          59                            80
  MALE                            49                            69
[1] 2 2
[1] FALSE
D29V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    66  39
  DEL PEAK  4(2Q37.3) WILD-TYPE 113  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     66   39
  DEL PEAK  4(2Q37.3) WILD-TYPE  113   33
     clus
vv    DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  NO                           66                           113
  YES                          39                            33
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  4(2Q37.3) MUTATED                             17             0
  DEL PEAK  4(2Q37.3) WILD-TYPE                           42             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  4(2Q37.3) MUTATED                                                                          0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK  4(2Q37.3) MUTATED                     45
  DEL PEAK  4(2Q37.3) WILD-TYPE                   58
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  4(2Q37.3) MUTATED                                                  2
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK  4(2Q37.3) MUTATED                 15
  DEL PEAK  4(2Q37.3) WILD-TYPE                9
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  4(2Q37.3) MUTATED                                                         18
  DEL PEAK  4(2Q37.3) WILD-TYPE                                                       10
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  4(2Q37.3) MUTATED                                          0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  4(2Q37.3) MUTATED                             0
  DEL PEAK  4(2Q37.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  4(2Q37.3) MUTATED                               0
  DEL PEAK  4(2Q37.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  4(2Q37.3) MUTATED                                           11
  DEL PEAK  4(2Q37.3) WILD-TYPE                                         10
D29V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  4(2Q37.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      17
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              45
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                  15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        11
                                                                          clus
vv                                                                         DEL PEAK  4(2Q37.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        42
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                58
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                     9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          10
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  4(2Q37.3) MUTATED   62 30  3 13
  DEL PEAK  4(2Q37.3) WILD-TYPE 90 39  6 13
D29V7, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          62                            90
  R1                          30                            39
  R2                           3                             6
  RX                          13                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       2                        10    91
  DEL PEAK  4(2Q37.3) WILD-TYPE     4                         8   133
D29V8, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              91
                           clus
vv                          DEL PEAK  4(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     1  95
  DEL PEAK  4(2Q37.3) WILD-TYPE   4 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      1   95
  DEL PEAK  4(2Q37.3) WILD-TYPE    4  125
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           125
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q37.3) MUTATED   60 50
  DEL PEAK  5(2Q37.3) WILD-TYPE 99 48
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          110                           147 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           50                            48 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       34.68        16.18        67.20        34.36        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A 
       14.43        15.85        12.07       101.98        30.51        32.15 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM 
       52.11        26.93        28.21        22.62        11.70         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR 
       18.08        20.94        17.52        50.01        19.69        88.57 
TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KY 
       44.91        14.37        42.84        18.64        26.56        12.85 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LW TCGA-DX-A3M1 
       18.54        54.21        85.02         6.28       136.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       31.86        51.02        14.99        50.43        34.88        85.45 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       26.47        59.84        15.95        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN 
       78.28        50.50        16.87        21.30        62.20        30.35 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT 
       61.97        45.14        47.87        38.17        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T 
       36.69        60.66        12.00        86.10        66.74        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
      106.55        50.40        21.70        20.32        19.89        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ 
       34.88         4.57         9.80        80.48         3.22        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       37.12       171.09        13.58        16.41         1.05         3.91 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-N1-A6IA 
       62.17        23.38        63.81        16.41        35.28         7.36 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       81.01        13.08        17.65        10.52        18.94         3.88 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX 
       22.82         8.61        10.72        12.46        84.79        38.27 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD 
       22.62         8.58        63.35        26.43        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 
       35.18        19.17 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2W 
       36.30        31.53        75.32        14.07        40.60       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z 
       13.28        22.85        60.00        84.66        16.60        37.02 
TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QQ-A8VB 
       12.62        52.27       159.29        17.75         8.28       188.15 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT 
       26.17        41.49        35.08        53.49        68.55        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       25.25        10.32        38.47        36.03         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       32.71        68.61        45.11        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       33.44        35.77         4.54        10.68        73.87        68.55 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
      108.82        37.58        37.41        82.68        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       36.85        26.99        86.30        64.21       101.23        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BO 
      152.12        29.49        48.20        20.05         9.34        40.77 
TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
      150.35        19.43         6.58         1.15        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       65.98         9.21        50.89        71.31        49.15        31.13 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK 
       15.48         8.05        33.30         0.72        19.53         1.38 
TCGA-IF-A4AJ TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       25.22        85.97         5.92       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       17.36         5.19        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
      122.96        37.55        38.63         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
        0.72        16.77        25.35        32.75        19.63        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-X6-A7WA TCGA-X6-A7WC 
       13.41        11.93         4.80        65.46        35.90        45.34 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         1.05                          0.49 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       171.09                        188.15 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        27.44                         33.44 
[1] "1.1 - 171.1 (27.4)" "0.5 - 188.2 (33.4)"
[1] "hr=" "1.5"
D30V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  5(2Q37.3) MUTATED                0                  4
  DEL PEAK  5(2Q37.3) WILD-TYPE              1                  3
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  5(2Q37.3) MUTATED                     0                   0
  DEL PEAK  5(2Q37.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                               1
  DEL PEAK  5(2Q37.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  5(2Q37.3) MUTATED                       1                     20
  DEL PEAK  5(2Q37.3) WILD-TYPE                     0                      8
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  5(2Q37.3) MUTATED                      1                    0
  DEL PEAK  5(2Q37.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                                       0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  5(2Q37.3) MUTATED                                  0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                                                1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  5(2Q37.3) MUTATED                                 2
  DEL PEAK  5(2Q37.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  5(2Q37.3) MUTATED                                         0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  5(2Q37.3) MUTATED                              0
  DEL PEAK  5(2Q37.3) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK  5(2Q37.3) MUTATED                         0
  DEL PEAK  5(2Q37.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  5(2Q37.3) MUTATED                                  5
  DEL PEAK  5(2Q37.3) WILD-TYPE                               12
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                                         5
  DEL PEAK  5(2Q37.3) WILD-TYPE                                       0
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  5(2Q37.3) MUTATED                             22
  DEL PEAK  5(2Q37.3) WILD-TYPE                           22
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  5(2Q37.3) MUTATED                                         1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  5(2Q37.3) MUTATED                                           1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  5(2Q37.3) MUTATED                                                  0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  5(2Q37.3) MUTATED                                          3
  DEL PEAK  5(2Q37.3) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                                                         0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  5(2Q37.3) MUTATED                                            1
  DEL PEAK  5(2Q37.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  5(2Q37.3) MUTATED                                                  29
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                44
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  5(2Q37.3) MUTATED                                                    0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  5(2Q37.3) MUTATED                                    2
  DEL PEAK  5(2Q37.3) WILD-TYPE                                  0
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK  5(2Q37.3) MUTATED                          3
  DEL PEAK  5(2Q37.3) WILD-TYPE                        2
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  5(2Q37.3) MUTATED                             2
  DEL PEAK  5(2Q37.3) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK  5(2Q37.3) MUTATED                           0
  DEL PEAK  5(2Q37.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  5(2Q37.3) MUTATED                                   3
  DEL PEAK  5(2Q37.3) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  5(2Q37.3) MUTATED                                   3
  DEL PEAK  5(2Q37.3) WILD-TYPE                                 2
D30V3, multiclass
                                                         clus
vv                                                        DEL PEAK  5(2Q37.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                4
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           20
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           5
  LOWER EXTREMITY - THIGH/KNEE                                                     22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                29
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          3
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        DEL PEAK  5(2Q37.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                              8
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             0
  LOWER EXTREMITY - THIGH/KNEE                                                       22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  44
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  0
  SUPERFICIAL TRUNK - BACK                                                            2
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   62 48
  DEL PEAK  5(2Q37.3) WILD-TYPE 77 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     62   48
  DEL PEAK  5(2Q37.3) WILD-TYPE   77   70
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                          62                            77
  MALE                            48                            70
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    70  37
  DEL PEAK  5(2Q37.3) WILD-TYPE 109  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     70   37
  DEL PEAK  5(2Q37.3) WILD-TYPE  109   35
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           70                           109
  YES                          37                            35
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  5(2Q37.3) MUTATED                             19             0
  DEL PEAK  5(2Q37.3) WILD-TYPE                           40             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  5(2Q37.3) MUTATED                                                                          0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK  5(2Q37.3) MUTATED                     45
  DEL PEAK  5(2Q37.3) WILD-TYPE                   58
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  5(2Q37.3) MUTATED                                                  2
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK  5(2Q37.3) MUTATED                 15
  DEL PEAK  5(2Q37.3) WILD-TYPE                9
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  5(2Q37.3) MUTATED                                                         17
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                       11
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  5(2Q37.3) MUTATED                                          0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  5(2Q37.3) MUTATED                             0
  DEL PEAK  5(2Q37.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  5(2Q37.3) MUTATED                               0
  DEL PEAK  5(2Q37.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  5(2Q37.3) MUTATED                                           12
  DEL PEAK  5(2Q37.3) WILD-TYPE                                          9
D30V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  5(2Q37.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      19
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              45
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                  15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        12
                                                                          clus
vv                                                                         DEL PEAK  5(2Q37.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        40
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                58
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                     9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  5(2Q37.3) MUTATED   61 31  4 14
  DEL PEAK  5(2Q37.3) WILD-TYPE 91 38  5 12
D30V7, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          61                            91
  R1                          31                            38
  R2                           4                             5
  RX                          14                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED       2                        10    93
  DEL PEAK  5(2Q37.3) WILD-TYPE     4                         8   131
D30V8, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              93
                           clus
vv                          DEL PEAK  5(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     2  95
  DEL PEAK  5(2Q37.3) WILD-TYPE   3 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      2   95
  DEL PEAK  5(2Q37.3) WILD-TYPE    3  125
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           125
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  6(3P21.31) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3P21.31) MUTATED    43  22
  DEL PEAK  6(3P21.31) WILD-TYPE 116  76
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            65                            192 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            22                             76 
$`DEL PEAK  6(3P21.31) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB32 
       34.68        34.36        17.95        40.60        13.28       101.98 
TCGA-DX-AB35 TCGA-FX-A3NK TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-QQ-A8VB TCGA-SG-A849 
       30.51        16.60        22.62        17.75       188.15        17.52 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 
       41.49        35.08        68.61        12.85        18.54        85.02 
TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YQ 
        9.04        33.44        44.68        35.28        15.95         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A8BK 
       41.00        78.28        86.30        30.35       152.12        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
       45.14        47.87        40.77       150.35        40.44        36.69 
TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B 
        6.58        15.72        86.10        77.88       106.55        50.89 
TCGA-DX-AB3C TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ 
       71.31        21.70         4.57         0.72         3.22        19.89 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A6RU TCGA-KD-A5QS 
      171.09         5.92        16.41         1.05        23.38        63.81 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A8VF TCGA-QQ-A8VH 
       10.45         7.36        37.55        17.65       111.98        10.52 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-VT-A80G TCGA-VT-AB3D TCGA-X6-A8C7 
       16.77        18.94        10.72        12.46        29.46 

$`DEL PEAK  6(3P21.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       14.43        14.07        15.85        12.07       106.45        22.85 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       60.00        84.66        32.15        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 
       26.93        52.27        28.21       159.29        11.70         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HL 
        6.35        18.08        20.94        26.17        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 
       26.56         0.56        14.04        32.71        45.11        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 
       79.17        49.05        86.83       136.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       26.99        50.50        16.87        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       34.49        62.20        29.49        48.20        20.05         9.34 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       38.17        27.95        60.66        19.43         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-FX-A2QS 
       12.00        65.98        66.74         9.21        50.40        49.15 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
       34.88        33.30         9.80        80.48        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN 
       37.12        25.22        13.58        85.97         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT 
       53.33        62.17       123.78        17.36         5.19        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       14.99        17.98        22.39        11.57       122.96        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        13.08         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
       35.90        37.12       130.32        64.77         0.72         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       22.82        25.35        32.75         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       13.41        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                         30.51                          31.33 
[1] "0.7 - 188.2 (30.5)" "0.5 - 159.3 (31.3)"
[1] "hr=" "1.2"
D31V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  6(3P21.31) MUTATED                0                  3
  DEL PEAK  6(3P21.31) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  6(3P21.31) MUTATED                     0                   0
  DEL PEAK  6(3P21.31) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  6(3P21.31) MUTATED                               1
  DEL PEAK  6(3P21.31) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  6(3P21.31) MUTATED                       1                      6
  DEL PEAK  6(3P21.31) WILD-TYPE                     0                     22
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  6(3P21.31) MUTATED                      0                    0
  DEL PEAK  6(3P21.31) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  6(3P21.31) MUTATED                                       0
  DEL PEAK  6(3P21.31) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  6(3P21.31) MUTATED                                  0
  DEL PEAK  6(3P21.31) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  6(3P21.31) MUTATED                                                0
  DEL PEAK  6(3P21.31) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  6(3P21.31) MUTATED                                 4
  DEL PEAK  6(3P21.31) WILD-TYPE                               6
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  6(3P21.31) MUTATED                                         0
  DEL PEAK  6(3P21.31) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  6(3P21.31) MUTATED                              2
  DEL PEAK  6(3P21.31) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK  6(3P21.31) MUTATED                         0
  DEL PEAK  6(3P21.31) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  6(3P21.31) MUTATED                                  5
  DEL PEAK  6(3P21.31) WILD-TYPE                               12
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  6(3P21.31) MUTATED                                         3
  DEL PEAK  6(3P21.31) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  6(3P21.31) MUTATED                             12
  DEL PEAK  6(3P21.31) WILD-TYPE                           32
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  6(3P21.31) MUTATED                                         0
  DEL PEAK  6(3P21.31) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  6(3P21.31) MUTATED                                           1
  DEL PEAK  6(3P21.31) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  6(3P21.31) MUTATED                                                  1
  DEL PEAK  6(3P21.31) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  6(3P21.31) MUTATED                                          2
  DEL PEAK  6(3P21.31) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  6(3P21.31) MUTATED                                                         0
  DEL PEAK  6(3P21.31) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  6(3P21.31) MUTATED                                            0
  DEL PEAK  6(3P21.31) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  6(3P21.31) MUTATED                                                  12
  DEL PEAK  6(3P21.31) WILD-TYPE                                                61
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  6(3P21.31) MUTATED                                                    0
  DEL PEAK  6(3P21.31) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  6(3P21.31) MUTATED                                    0
  DEL PEAK  6(3P21.31) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK  6(3P21.31) MUTATED                          1
  DEL PEAK  6(3P21.31) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  6(3P21.31) MUTATED                             4
  DEL PEAK  6(3P21.31) WILD-TYPE                           0
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK  6(3P21.31) MUTATED                           1
  DEL PEAK  6(3P21.31) WILD-TYPE                         0
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  6(3P21.31) MUTATED                                   4
  DEL PEAK  6(3P21.31) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  6(3P21.31) MUTATED                                   2
  DEL PEAK  6(3P21.31) WILD-TYPE                                 3
D31V3, multiclass
                                                         clus
vv                                                        DEL PEAK  6(3P21.31) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                             6
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK  6(3P21.31) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              22
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          0
  SUPERFICIAL TRUNK - FLANK                                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED    36  29
  DEL PEAK  6(3P21.31) WILD-TYPE 103  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED     36   29
  DEL PEAK  6(3P21.31) WILD-TYPE  103   89
        clus
vv       DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  FEMALE                           36                            103
  MALE                             29                             89
[1] 2 2
[1] FALSE
D31V5, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED    39  25
  DEL PEAK  6(3P21.31) WILD-TYPE 140  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED     39   25
  DEL PEAK  6(3P21.31) WILD-TYPE  140   47
     clus
vv    DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  NO                            39                            140
  YES                           25                             47
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  6(3P21.31) MUTATED                             12             0
  DEL PEAK  6(3P21.31) WILD-TYPE                           47             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  6(3P21.31) MUTATED                                                                          0
  DEL PEAK  6(3P21.31) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK  6(3P21.31) MUTATED                     15
  DEL PEAK  6(3P21.31) WILD-TYPE                   88
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  6(3P21.31) MUTATED                                                  3
  DEL PEAK  6(3P21.31) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK  6(3P21.31) MUTATED                 11
  DEL PEAK  6(3P21.31) WILD-TYPE               13
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  6(3P21.31) MUTATED                                                         12
  DEL PEAK  6(3P21.31) WILD-TYPE                                                       16
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  6(3P21.31) MUTATED                                          0
  DEL PEAK  6(3P21.31) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  6(3P21.31) MUTATED                             2
  DEL PEAK  6(3P21.31) WILD-TYPE                           0
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  6(3P21.31) MUTATED                               3
  DEL PEAK  6(3P21.31) WILD-TYPE                             3
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  6(3P21.31) MUTATED                                            7
  DEL PEAK  6(3P21.31) WILD-TYPE                                         14
D31V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  6(3P21.31) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       12
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       3
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          7
                                                                          clus
vv                                                                         DEL PEAK  6(3P21.31) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         47
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         3
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  6(3P21.31) MUTATED    37  15   4   8
  DEL PEAK  6(3P21.31) WILD-TYPE 115  54   5  18
D31V7, multiclass
    clus
vv   DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  R0                           37                            115
  R1                           15                             54
  R2                            4                              5
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P21.31) MUTATED       2                         6    55
  DEL PEAK  6(3P21.31) WILD-TYPE     4                        12   169
D31V8, multiclass
                           clus
vv                          DEL PEAK  6(3P21.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               55
                           clus
vv                          DEL PEAK  6(3P21.31) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED     1  55
  DEL PEAK  6(3P21.31) WILD-TYPE   4 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED      1   55
  DEL PEAK  6(3P21.31) WILD-TYPE    4  165
                        clus
vv                       DEL PEAK  6(3P21.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK  6(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  7(3Q13.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(3Q13.31) MUTATED    29  22
  DEL PEAK  7(3Q13.31) WILD-TYPE 130  76
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            51                            206 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            22                             76 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK 
       34.68        14.43       106.45        30.51        60.00        16.60 
TCGA-HB-A43Z TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-3B-A9HL TCGA-DX-A1KU 
       37.02        17.75         6.35       188.15        19.69        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LY 
       32.71        68.61        18.54        74.66        49.05        33.44 
TCGA-DX-A3M1 TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-AATS 
       44.68        15.95        41.00        21.30       152.12         1.15 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N8 
       71.31        49.15        20.32        19.89         4.57         0.72 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IW-A3M5 TCGA-K1-A42X TCGA-K1-A6RU TCGA-MB-A5Y8 
        3.22        19.89         5.92       123.78        23.38        25.41 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-RN-AAAQ 
       21.73        14.99        10.45        37.55        13.08        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-AB3D TCGA-WP-A9GB TCGA-X6-A7W8 
        3.88        32.75        19.63        12.46         8.58        26.43 
TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X9-A971 
       45.34        20.65        27.32 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.07        15.85        40.60        12.07 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 
       13.28        22.85       101.98        84.66        32.15        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70         8.28        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        50.01        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY 
       38.47        36.03        18.64        26.56         0.56        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       45.11        54.21        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        95.38        79.17         9.04        86.83       136.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99         3.06        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        86.30        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20        30.35        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A3NJ 
        9.21        77.88       106.55        50.40        50.89        31.13 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
       21.70        15.48         8.05        67.63        34.88        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48        19.53         1.38        37.12        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      171.09        13.58        85.97        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS 
      101.26        53.33        62.17        17.36         5.19        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       16.41        35.28        30.31         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
       18.94        22.82        25.35         8.61        13.22        13.41 
TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62        63.35        35.90        18.08        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        188.15                         171.09 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        21.300                         33.945 
[1] "0.7 - 188.2 (21.3)" "0.5 - 171.1 (33.9)"
[1] "hr=" "1.4"
D32V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  7(3Q13.31) MUTATED                0                  3
  DEL PEAK  7(3Q13.31) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  7(3Q13.31) MUTATED                     0                   0
  DEL PEAK  7(3Q13.31) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  7(3Q13.31) MUTATED                               0
  DEL PEAK  7(3Q13.31) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  7(3Q13.31) MUTATED                       0                      6
  DEL PEAK  7(3Q13.31) WILD-TYPE                     1                     22
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  7(3Q13.31) MUTATED                      1                    0
  DEL PEAK  7(3Q13.31) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  7(3Q13.31) MUTATED                                       0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  7(3Q13.31) MUTATED                                  0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  7(3Q13.31) MUTATED                                                1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  7(3Q13.31) MUTATED                                 1
  DEL PEAK  7(3Q13.31) WILD-TYPE                               9
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  7(3Q13.31) MUTATED                                         0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  7(3Q13.31) MUTATED                              0
  DEL PEAK  7(3Q13.31) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK  7(3Q13.31) MUTATED                         0
  DEL PEAK  7(3Q13.31) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  7(3Q13.31) MUTATED                                  3
  DEL PEAK  7(3Q13.31) WILD-TYPE                               14
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  7(3Q13.31) MUTATED                                         1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                       4
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  7(3Q13.31) MUTATED                              9
  DEL PEAK  7(3Q13.31) WILD-TYPE                           35
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  7(3Q13.31) MUTATED                                         0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  7(3Q13.31) MUTATED                                           1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  7(3Q13.31) MUTATED                                                  1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  7(3Q13.31) MUTATED                                          2
  DEL PEAK  7(3Q13.31) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  7(3Q13.31) MUTATED                                                         1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  7(3Q13.31) MUTATED                                            0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  7(3Q13.31) MUTATED                                                  12
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                61
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  7(3Q13.31) MUTATED                                                    0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  7(3Q13.31) MUTATED                                    1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK  7(3Q13.31) MUTATED                          0
  DEL PEAK  7(3Q13.31) WILD-TYPE                        5
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  7(3Q13.31) MUTATED                             2
  DEL PEAK  7(3Q13.31) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK  7(3Q13.31) MUTATED                           1
  DEL PEAK  7(3Q13.31) WILD-TYPE                         0
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  7(3Q13.31) MUTATED                                   3
  DEL PEAK  7(3Q13.31) WILD-TYPE                                 4
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  7(3Q13.31) MUTATED                                   2
  DEL PEAK  7(3Q13.31) WILD-TYPE                                 3
D32V3, multiclass
                                                         clus
vv                                                        DEL PEAK  7(3Q13.31) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             6
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            1
  LOWER EXTREMITY - THIGH/KNEE                                                       9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK  7(3Q13.31) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              22
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              4
  LOWER EXTREMITY - THIGH/KNEE                                                        35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED    25  26
  DEL PEAK  7(3Q13.31) WILD-TYPE 114  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED     25   26
  DEL PEAK  7(3Q13.31) WILD-TYPE  114   92
        clus
vv       DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  FEMALE                           25                            114
  MALE                             26                             92
[1] 2 2
[1] FALSE
D32V5, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED    29  21
  DEL PEAK  7(3Q13.31) WILD-TYPE 150  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED     29   21
  DEL PEAK  7(3Q13.31) WILD-TYPE  150   51
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                            29                            150
  YES                           21                             51
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  7(3Q13.31) MUTATED                             15             0
  DEL PEAK  7(3Q13.31) WILD-TYPE                           44             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  7(3Q13.31) MUTATED                                                                          0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK  7(3Q13.31) MUTATED                     13
  DEL PEAK  7(3Q13.31) WILD-TYPE                   90
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  7(3Q13.31) MUTATED                                                  4
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                5
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK  7(3Q13.31) MUTATED                  3
  DEL PEAK  7(3Q13.31) WILD-TYPE               21
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  7(3Q13.31) MUTATED                                                          7
  DEL PEAK  7(3Q13.31) WILD-TYPE                                                       21
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  7(3Q13.31) MUTATED                                          0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  7(3Q13.31) MUTATED                             1
  DEL PEAK  7(3Q13.31) WILD-TYPE                           1
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  7(3Q13.31) MUTATED                               1
  DEL PEAK  7(3Q13.31) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  7(3Q13.31) MUTATED                                            7
  DEL PEAK  7(3Q13.31) WILD-TYPE                                         14
D32V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  7(3Q13.31) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       15
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    4
  MYXOFIBROSARCOMA                                                                                    3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          7
                                                                          clus
vv                                                                         DEL PEAK  7(3Q13.31) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         44
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 90
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      5
  MYXOFIBROSARCOMA                                                                                     21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  7(3Q13.31) MUTATED    24  15   4   7
  DEL PEAK  7(3Q13.31) WILD-TYPE 128  54   5  19
D32V7, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                           24                            128
  R1                           15                             54
  R2                            4                              5
  RX                            7                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q13.31) MUTATED       1                         2    47
  DEL PEAK  7(3Q13.31) WILD-TYPE     5                        16   177
D32V8, multiclass
                           clus
vv                          DEL PEAK  7(3Q13.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               47
                           clus
vv                          DEL PEAK  7(3Q13.31) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  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"
D32V9, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     1  45
  DEL PEAK  7(3Q13.31) WILD-TYPE   4 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   45
  DEL PEAK  7(3Q13.31) WILD-TYPE    4  175
                        clus
vv                       DEL PEAK  7(3Q13.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       DEL PEAK  7(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            175
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  8(3Q29) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  8(3Q29) MUTATED    32  22
  DEL PEAK  8(3Q29) WILD-TYPE 127  76
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         54                         203 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         22                          76 
$`DEL PEAK  8(3Q29) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK 
       31.53        34.68       106.45        30.51        60.00        16.60 
TCGA-HB-A43Z TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-3B-A9HL TCGA-DX-A1KW 
       37.02        17.75         6.35       188.15        19.69        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A3LT 
       68.61        12.85        18.54        54.21        74.66        49.05 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O 
       33.44        44.68        10.68        85.45        24.26        52.77 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YS TCGA-DX-A7EO TCGA-DX-A8BL TCGA-DX-A8BR 
       26.47        15.95        78.28       152.12        45.14       150.35 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EJ 
       71.31        49.15        20.32         4.57        80.48         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-K1-A6RU TCGA-MB-A8JK TCGA-MJ-A68H 
       19.89        37.12        13.58        23.38        21.73        14.99 
TCGA-PC-A5DL TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-SI-A71Q TCGA-VT-A80G TCGA-VT-AB3D 
       37.55        48.59        18.94        32.75        10.72        12.46 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X9-A971 TCGA-Z4-AAPG 
       65.46         8.58        45.34        20.65        27.32        15.98 

$`DEL PEAK  8(3Q29) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        16.18        67.20        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 
       13.28        22.85       101.98        84.66        32.15        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70         8.28        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        50.01        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       45.11        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
       95.38        79.17         9.04        86.83       136.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48P 
       50.43        34.88         9.73        45.99        35.28        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       50.50        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        62.20        30.35        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS 
        9.34        61.97        47.87        38.17        40.77        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       40.44        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A3NJ 
        9.21        77.88       106.55        50.40        50.89        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       21.70        19.89        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       33.30         0.72         9.80        19.53         1.38        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      171.09        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        18.08        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       64.77        10.52         0.72        16.77         3.88        22.82 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
       25.35         8.61        19.63        13.22        13.41        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 
        4.80        84.79        38.27        22.62        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       35.90        18.08        30.84        35.18        19.17        50.86 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                       3.22                        0.49 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                     188.15                      171.09 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                      32.12                       30.84 
[1] "3.2 - 188.2 (32.1)" "0.5 - 171.1 (30.8)"
[1] "hr=" "1"  
D33V2, continuous
                             vv
clus                          CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  8(3Q29) MUTATED                0                  2
  DEL PEAK  8(3Q29) WILD-TYPE              1                  5
                             vv
clus                          CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  8(3Q29) MUTATED                     0                   0
  DEL PEAK  8(3Q29) WILD-TYPE                   2                   1
                             vv
clus                          CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  8(3Q29) MUTATED                               0
  DEL PEAK  8(3Q29) WILD-TYPE                             2
                             vv
clus                          GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  8(3Q29) MUTATED                       0                      3
  DEL PEAK  8(3Q29) WILD-TYPE                     1                     25
                             vv
clus                          HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  8(3Q29) MUTATED                      0                    0
  DEL PEAK  8(3Q29) WILD-TYPE                    2                    1
                             vv
clus                          HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  8(3Q29) MUTATED                                       0
  DEL PEAK  8(3Q29) WILD-TYPE                                     2
                             vv
clus                          LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  8(3Q29) MUTATED                                  0
  DEL PEAK  8(3Q29) WILD-TYPE                                1
                             vv
clus                          LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  8(3Q29) MUTATED                                                1
  DEL PEAK  8(3Q29) WILD-TYPE                                              1
                             vv
clus                          LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  8(3Q29) MUTATED                                 1
  DEL PEAK  8(3Q29) WILD-TYPE                               9
                             vv
clus                          LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  8(3Q29) MUTATED                                         0
  DEL PEAK  8(3Q29) WILD-TYPE                                       2
                             vv
clus                          LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  8(3Q29) MUTATED                              1
  DEL PEAK  8(3Q29) WILD-TYPE                            3
                             vv
clus                          LOWER EXTREMITY - GROIN
  DEL PEAK  8(3Q29) MUTATED                         1
  DEL PEAK  8(3Q29) WILD-TYPE                       1
                             vv
clus                          LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  8(3Q29) MUTATED                                  3
  DEL PEAK  8(3Q29) WILD-TYPE                               14
                             vv
clus                          LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  8(3Q29) MUTATED                                         3
  DEL PEAK  8(3Q29) WILD-TYPE                                       2
                             vv
clus                          LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  8(3Q29) MUTATED                              9
  DEL PEAK  8(3Q29) WILD-TYPE                           35
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  8(3Q29) MUTATED                                         0
  DEL PEAK  8(3Q29) WILD-TYPE                                       4
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  8(3Q29) MUTATED                                           1
  DEL PEAK  8(3Q29) WILD-TYPE                                         1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  8(3Q29) MUTATED                                                  1
  DEL PEAK  8(3Q29) WILD-TYPE                                                4
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  8(3Q29) MUTATED                                          1
  DEL PEAK  8(3Q29) WILD-TYPE                                        7
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  8(3Q29) MUTATED                                                         1
  DEL PEAK  8(3Q29) WILD-TYPE                                                       1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  8(3Q29) MUTATED                                            0
  DEL PEAK  8(3Q29) WILD-TYPE                                          1
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  8(3Q29) MUTATED                                                  17
  DEL PEAK  8(3Q29) WILD-TYPE                                                56
                             vv
clus                          RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  8(3Q29) MUTATED                                                    1
  DEL PEAK  8(3Q29) WILD-TYPE                                                  2
                             vv
clus                          SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  8(3Q29) MUTATED                                    0
  DEL PEAK  8(3Q29) WILD-TYPE                                  2
                             vv
clus                          SUPERFICIAL TRUNK - BACK
  DEL PEAK  8(3Q29) MUTATED                          0
  DEL PEAK  8(3Q29) WILD-TYPE                        5
                             vv
clus                          SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  8(3Q29) MUTATED                             2
  DEL PEAK  8(3Q29) WILD-TYPE                           2
                             vv
clus                          SUPERFICIAL TRUNK - FLANK
  DEL PEAK  8(3Q29) MUTATED                           1
  DEL PEAK  8(3Q29) WILD-TYPE                         0
                             vv
clus                          UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  8(3Q29) MUTATED                                   3
  DEL PEAK  8(3Q29) WILD-TYPE                                 4
                             vv
clus                          UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  8(3Q29) MUTATED                                   2
  DEL PEAK  8(3Q29) WILD-TYPE                                 3
D33V3, multiclass
                                                         clus
vv                                                        DEL PEAK  8(3Q29) MUTATED
  CHEST - BREAST                                                                  0
  CHEST - CHEST WALL                                                              2
  CHEST - LUNG/PLEURA                                                             0
  CHEST - MEDIASTINUM                                                             0
  CHEST - OTHER (PLEASE SPECIFY                                                   0
  GYNECOLOGICAL - OVARY                                                           0
  GYNECOLOGICAL - UTERUS                                                          3
  HEAD AND NECK - HEAD                                                            0
  HEAD AND NECK - NECK                                                            0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                           0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                 1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                         0
  LOWER EXTREMITY - FOOT/ANKLE                                                    1
  LOWER EXTREMITY - GROIN                                                         1
  LOWER EXTREMITY - LOWER LEG/CALF                                                3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                         3
  LOWER EXTREMITY - THIGH/KNEE                                                    9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                       1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                         1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                      0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                              17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                              1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                              0
  SUPERFICIAL TRUNK - BACK                                                        0
  SUPERFICIAL TRUNK - BUTTOCK                                                     2
  SUPERFICIAL TRUNK - FLANK                                                       1
  UPPER EXTREMITY - SHOULDER/AXILLA                                               3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                               2
                                                         clus
vv                                                        DEL PEAK  8(3Q29) WILD-TYPE
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                5
  CHEST - LUNG/PLEURA                                                               2
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           25
  HEAD AND NECK - HEAD                                                              2
  HEAD AND NECK - NECK                                                              1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           2
  LOWER EXTREMITY - FOOT/ANKLE                                                      3
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          5
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED    26  28
  DEL PEAK  8(3Q29) WILD-TYPE 113  90
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     26   28
  DEL PEAK  8(3Q29) WILD-TYPE  113   90
        clus
vv       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  FEMALE                        26                         113
  MALE                          28                          90
[1] 2 2
[1] FALSE
D33V5, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED    33  20
  DEL PEAK  8(3Q29) WILD-TYPE 146  52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     33   20
  DEL PEAK  8(3Q29) WILD-TYPE  146   52
     clus
vv    DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  NO                         33                         146
  YES                        20                          52
[1] 2 2
[1] FALSE
                             vv
clus                          DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  8(3Q29) MUTATED                             17             0
  DEL PEAK  8(3Q29) WILD-TYPE                           42             2
                             vv
clus                          GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  8(3Q29) MUTATED                                                                          0
  DEL PEAK  8(3Q29) WILD-TYPE                                                                        1
                             vv
clus                          LEIOMYOSARCOMA (LMS)
  DEL PEAK  8(3Q29) MUTATED                     17
  DEL PEAK  8(3Q29) WILD-TYPE                   86
                             vv
clus                          MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  8(3Q29) MUTATED                                                  2
  DEL PEAK  8(3Q29) WILD-TYPE                                                7
                             vv
clus                          MYXOFIBROSARCOMA
  DEL PEAK  8(3Q29) MUTATED                  2
  DEL PEAK  8(3Q29) WILD-TYPE               22
                             vv
clus                          PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  8(3Q29) MUTATED                                                          6
  DEL PEAK  8(3Q29) WILD-TYPE                                                       22
                             vv
clus                          SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  8(3Q29) MUTATED                                          0
  DEL PEAK  8(3Q29) WILD-TYPE                                        2
                             vv
clus                          SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  8(3Q29) MUTATED                             1
  DEL PEAK  8(3Q29) WILD-TYPE                           1
                             vv
clus                          SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  8(3Q29) MUTATED                               1
  DEL PEAK  8(3Q29) WILD-TYPE                             5
                             vv
clus                          UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  8(3Q29) MUTATED                                            8
  DEL PEAK  8(3Q29) WILD-TYPE                                         13
D33V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  8(3Q29) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                    17
  DESMOID TUMOR                                                                                    0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                         0
  LEIOMYOSARCOMA (LMS)                                                                            17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                 2
  MYXOFIBROSARCOMA                                                                                 2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                         0
  SYNOVIAL SARCOMA - BIPHASIC                                                                      1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                    1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                       8
                                                                          clus
vv                                                                         DEL PEAK  8(3Q29) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                      42
  DESMOID TUMOR                                                                                      2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           1
  LEIOMYOSARCOMA (LMS)                                                                              86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   7
  MYXOFIBROSARCOMA                                                                                  22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          22
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           2
  SYNOVIAL SARCOMA - BIPHASIC                                                                        1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  8(3Q29) MUTATED    29  19   2   4
  DEL PEAK  8(3Q29) WILD-TYPE 123  50   7  22
D33V7, multiclass
    clus
vv   DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  R0                        29                         123
  R1                        19                          50
  R2                         2                           7
  RX                         4                          22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q29) MUTATED       0                         2    52
  DEL PEAK  8(3Q29) WILD-TYPE     6                        16   172
D33V8, multiclass
                           clus
vv                          DEL PEAK  8(3Q29) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            52
                           clus
vv                          DEL PEAK  8(3Q29) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED     1  48
  DEL PEAK  8(3Q29) WILD-TYPE   4 172
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED      1   48
  DEL PEAK  8(3Q29) WILD-TYPE    4  172
                        clus
vv                       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        48                         172
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q35.1) MUTATED    54  40
  DEL PEAK  9(4Q35.1) WILD-TYPE 105  58
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           94                           163 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           40                            58 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H 
       34.68        67.20        34.36        17.95        14.07        15.85 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IW-A3M6 
       12.07       106.45       101.98        37.02        26.93        22.62 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J 
       11.70         6.35        18.08        20.94       188.15        26.17 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-3R-A8YX 
       35.08        50.01        19.69        88.57        26.56         0.56 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ 
       68.61        12.85        54.21        74.66         6.28         8.58 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD 
        9.04        49.05       136.44         4.54        14.99        50.43 
TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR 
       34.88        24.26        26.47        82.68         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       78.28        16.87        64.21        21.30        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
       38.17        27.95        40.44        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2Z 
        1.15        17.79        12.00        86.10       106.55        50.40 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A4EK 
       49.15        20.32        67.63         0.72         3.22         1.38 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W 
       25.22        13.58         5.92        16.41         1.05        62.17 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A8JK TCGA-MO-A47R TCGA-QQ-A5V9 
        5.19        63.81        35.28        21.73        10.45        46.82 
TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XO 
       10.52        18.94        22.82        19.63        13.41        11.93 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       84.79        65.46         8.58        26.43        35.90        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       30.84        35.18        19.17        20.65 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        31.53        16.18        75.32        15.22        14.43 
TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       40.60        13.28        22.85        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 
       32.15        16.60        12.62        52.11        52.27        28.21 
TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HP 
      159.29        17.75         8.28        17.52        41.49        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       68.55        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1KW 
       10.32        38.47        36.03        18.64        14.04        32.71 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       45.11        18.54        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       79.17        86.83        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J 
       51.02        10.68        73.87        68.55        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       45.99        35.28        52.77        46.03       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        15.95        37.41        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI 
       36.85        26.99        50.50        86.30       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-AB2G 
        9.34        61.97        40.77       150.35        19.43        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        66.74         9.21        77.88        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       31.13        21.70        19.89        15.48         8.05        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ 
        4.57        33.30         9.80        80.48        19.53        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       37.12       171.09        85.97         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
      123.78        17.36        23.38        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        22.39        11.57 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        7.36       122.96        37.55        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
      130.32       111.98        64.77         0.72        16.77         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D 
       25.35        32.75         8.61        13.22        10.72        12.46 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 
        4.80        38.27        22.62        63.35        18.08        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       188.15                        171.09 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        26.30                         32.75 
[1] "0.6 - 188.2 (26.3)" "0.5 - 171.1 (32.8)"
[1] "hr=" "1.4"
D34V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK  9(4Q35.1) MUTATED                0                  3
  DEL PEAK  9(4Q35.1) WILD-TYPE              1                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK  9(4Q35.1) MUTATED                     0                   0
  DEL PEAK  9(4Q35.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK  9(4Q35.1) MUTATED                               2
  DEL PEAK  9(4Q35.1) WILD-TYPE                             0
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK  9(4Q35.1) MUTATED                       0                     10
  DEL PEAK  9(4Q35.1) WILD-TYPE                     1                     18
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK  9(4Q35.1) MUTATED                      0                    0
  DEL PEAK  9(4Q35.1) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK  9(4Q35.1) MUTATED                                       0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK  9(4Q35.1) MUTATED                                  0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK  9(4Q35.1) MUTATED                                                1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK  9(4Q35.1) MUTATED                                 4
  DEL PEAK  9(4Q35.1) WILD-TYPE                               6
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK  9(4Q35.1) MUTATED                                         1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK  9(4Q35.1) MUTATED                              0
  DEL PEAK  9(4Q35.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK  9(4Q35.1) MUTATED                         0
  DEL PEAK  9(4Q35.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK  9(4Q35.1) MUTATED                                  8
  DEL PEAK  9(4Q35.1) WILD-TYPE                                9
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK  9(4Q35.1) MUTATED                                         4
  DEL PEAK  9(4Q35.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK  9(4Q35.1) MUTATED                             23
  DEL PEAK  9(4Q35.1) WILD-TYPE                           21
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK  9(4Q35.1) MUTATED                                         0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK  9(4Q35.1) MUTATED                                           1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK  9(4Q35.1) MUTATED                                                  1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK  9(4Q35.1) MUTATED                                          2
  DEL PEAK  9(4Q35.1) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK  9(4Q35.1) MUTATED                                                         1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK  9(4Q35.1) MUTATED                                            1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK  9(4Q35.1) MUTATED                                                  20
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                53
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK  9(4Q35.1) MUTATED                                                    1
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK  9(4Q35.1) MUTATED                                    0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK  9(4Q35.1) MUTATED                          3
  DEL PEAK  9(4Q35.1) WILD-TYPE                        2
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK  9(4Q35.1) MUTATED                             2
  DEL PEAK  9(4Q35.1) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK  9(4Q35.1) MUTATED                           0
  DEL PEAK  9(4Q35.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK  9(4Q35.1) MUTATED                                   4
  DEL PEAK  9(4Q35.1) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK  9(4Q35.1) MUTATED                                   2
  DEL PEAK  9(4Q35.1) WILD-TYPE                                 3
D34V3, multiclass
                                                         clus
vv                                                        DEL PEAK  9(4Q35.1) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           10
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                20
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          3
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        DEL PEAK  9(4Q35.1) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       0
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             18
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  53
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            2
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   53 41
  DEL PEAK  9(4Q35.1) WILD-TYPE 86 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     53   41
  DEL PEAK  9(4Q35.1) WILD-TYPE   86   77
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          53                            86
  MALE                            41                            77
[1] 2 2
[1] FALSE
D34V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED    55  37
  DEL PEAK  9(4Q35.1) WILD-TYPE 124  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     55   37
  DEL PEAK  9(4Q35.1) WILD-TYPE  124   35
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                           55                           124
  YES                          37                            35
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK  9(4Q35.1) MUTATED                             17             0
  DEL PEAK  9(4Q35.1) WILD-TYPE                           42             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK  9(4Q35.1) MUTATED                                                                          0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK  9(4Q35.1) MUTATED                     34
  DEL PEAK  9(4Q35.1) WILD-TYPE                   69
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK  9(4Q35.1) MUTATED                                                  4
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                5
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK  9(4Q35.1) MUTATED                 15
  DEL PEAK  9(4Q35.1) WILD-TYPE                9
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK  9(4Q35.1) MUTATED                                                         16
  DEL PEAK  9(4Q35.1) WILD-TYPE                                                       12
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK  9(4Q35.1) MUTATED                                          0
  DEL PEAK  9(4Q35.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK  9(4Q35.1) MUTATED                             0
  DEL PEAK  9(4Q35.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK  9(4Q35.1) MUTATED                               0
  DEL PEAK  9(4Q35.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK  9(4Q35.1) MUTATED                                            8
  DEL PEAK  9(4Q35.1) WILD-TYPE                                         13
D34V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK  9(4Q35.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      17
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              34
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   4
  MYXOFIBROSARCOMA                                                                                  15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
                                                                          clus
vv                                                                         DEL PEAK  9(4Q35.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        42
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                69
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                     9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4Q35.1) MUTATED    52  32   3   7
  DEL PEAK  9(4Q35.1) WILD-TYPE 100  37   6  19
D34V7, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                          52                           100
  R1                          32                            37
  R2                           3                             6
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED       4                         6    79
  DEL PEAK  9(4Q35.1) WILD-TYPE     2                        12   145
D34V8, multiclass
                           clus
vv                          DEL PEAK  9(4Q35.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              79
                           clus
vv                          DEL PEAK  9(4Q35.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     0  83
  DEL PEAK  9(4Q35.1) WILD-TYPE   5 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      0   83
  DEL PEAK  9(4Q35.1) WILD-TYPE    5  137
                        clus
vv                       DEL PEAK  9(4Q35.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK  9(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           137
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 10(5P15.33) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(5P15.33) MUTATED    19  14
  DEL PEAK 10(5P15.33) WILD-TYPE 140  84
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            33                            224 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            14                             84 
$`DEL PEAK 10(5P15.33) MUTATED`
TCGA-DX-A6BK TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB32 TCGA-DX-AB36 TCGA-FX-A3NK 
       16.18        17.95        14.43       101.98        60.00        16.60 
TCGA-HB-A5W3 TCGA-KF-A41W TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9I0 TCGA-DX-A1L3 
       12.62        11.70        17.52        26.17        36.03        33.53 
TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A6YQ TCGA-DX-A8BJ 
       74.66        49.05        44.68        10.68         3.06         9.34 
TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-K1-A6RU TCGA-K1-A6RV 
        6.58        15.72        80.48       171.09        23.38         5.19 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VG 
       21.73        19.73        17.65        48.59        35.90        64.77 
TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A8C3 
       10.72        22.62        19.17 

$`DEL PEAK 10(5P15.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       15.22        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z 
       13.28        22.85        30.51        84.66        32.15        37.02 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        38.47        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       85.02        66.94         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        86.83       136.44        33.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        14.99        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        85.45         9.73        45.99        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       36.85        26.99        41.00        78.28        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       86.30        64.21       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       40.44        36.69        60.66        19.43         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       12.00        65.98        86.10        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI 
       34.88         4.57        33.30         0.72         9.80        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
        3.22         1.38        19.89        37.12        25.22        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33        62.17       123.78        17.36        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J 
       35.28        30.31        25.41         0.49        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        13.08         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        65.46         8.58        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 
       35.90        18.08        45.34        30.84        35.18        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                          3.06                           0.49 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                        171.09                         188.15 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                         19.73                          32.43 
[1] "3.1 - 171.1 (19.7)" "0.5 - 188.2 (32.4)"
[1] "hr=" "1.4"
D35V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 10(5P15.33) MUTATED                1                  4
  DEL PEAK 10(5P15.33) WILD-TYPE              0                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 10(5P15.33) MUTATED                     0                   0
  DEL PEAK 10(5P15.33) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 10(5P15.33) MUTATED                               0
  DEL PEAK 10(5P15.33) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 10(5P15.33) MUTATED                       0                      2
  DEL PEAK 10(5P15.33) WILD-TYPE                     1                     26
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 10(5P15.33) MUTATED                      0                    0
  DEL PEAK 10(5P15.33) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 10(5P15.33) MUTATED                                       0
  DEL PEAK 10(5P15.33) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 10(5P15.33) MUTATED                                  0
  DEL PEAK 10(5P15.33) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 10(5P15.33) MUTATED                                                0
  DEL PEAK 10(5P15.33) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 10(5P15.33) MUTATED                                 0
  DEL PEAK 10(5P15.33) WILD-TYPE                              10
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 10(5P15.33) MUTATED                                         0
  DEL PEAK 10(5P15.33) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 10(5P15.33) MUTATED                              1
  DEL PEAK 10(5P15.33) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 10(5P15.33) MUTATED                         1
  DEL PEAK 10(5P15.33) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 10(5P15.33) MUTATED                                  2
  DEL PEAK 10(5P15.33) WILD-TYPE                               15
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 10(5P15.33) MUTATED                                         2
  DEL PEAK 10(5P15.33) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 10(5P15.33) MUTATED                              6
  DEL PEAK 10(5P15.33) WILD-TYPE                           38
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 10(5P15.33) MUTATED                                         0
  DEL PEAK 10(5P15.33) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 10(5P15.33) MUTATED                                           1
  DEL PEAK 10(5P15.33) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 10(5P15.33) MUTATED                                                  0
  DEL PEAK 10(5P15.33) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 10(5P15.33) MUTATED                                          1
  DEL PEAK 10(5P15.33) WILD-TYPE                                        7
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 10(5P15.33) MUTATED                                                         0
  DEL PEAK 10(5P15.33) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 10(5P15.33) MUTATED                                            0
  DEL PEAK 10(5P15.33) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 10(5P15.33) MUTATED                                                   6
  DEL PEAK 10(5P15.33) WILD-TYPE                                                67
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 10(5P15.33) MUTATED                                                    0
  DEL PEAK 10(5P15.33) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 10(5P15.33) MUTATED                                    1
  DEL PEAK 10(5P15.33) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 10(5P15.33) MUTATED                          1
  DEL PEAK 10(5P15.33) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 10(5P15.33) MUTATED                             2
  DEL PEAK 10(5P15.33) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 10(5P15.33) MUTATED                           0
  DEL PEAK 10(5P15.33) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 10(5P15.33) MUTATED                                   0
  DEL PEAK 10(5P15.33) WILD-TYPE                                 7
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 10(5P15.33) MUTATED                                   2
  DEL PEAK 10(5P15.33) WILD-TYPE                                 3
D35V3, multiclass
                                                         clus
vv                                                        DEL PEAK 10(5P15.33) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             2
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                       6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  6
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK 10(5P15.33) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              26
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        38
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   67
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED    18  15
  DEL PEAK 10(5P15.33) WILD-TYPE 121 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED     18   15
  DEL PEAK 10(5P15.33) WILD-TYPE  121  103
        clus
vv       DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  FEMALE                           18                            121
  MALE                             15                            103
[1] 2 2
[1] FALSE
D35V5, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED    22  11
  DEL PEAK 10(5P15.33) WILD-TYPE 157  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED     22   11
  DEL PEAK 10(5P15.33) WILD-TYPE  157   61
     clus
vv    DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  NO                            22                            157
  YES                           11                             61
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 10(5P15.33) MUTATED                              8             0
  DEL PEAK 10(5P15.33) WILD-TYPE                           51             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 10(5P15.33) MUTATED                                                                          0
  DEL PEAK 10(5P15.33) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 10(5P15.33) MUTATED                     11
  DEL PEAK 10(5P15.33) WILD-TYPE                   92
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 10(5P15.33) MUTATED                                                  1
  DEL PEAK 10(5P15.33) WILD-TYPE                                                8
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 10(5P15.33) MUTATED                  5
  DEL PEAK 10(5P15.33) WILD-TYPE               19
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 10(5P15.33) MUTATED                                                          3
  DEL PEAK 10(5P15.33) WILD-TYPE                                                       25
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 10(5P15.33) MUTATED                                          0
  DEL PEAK 10(5P15.33) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 10(5P15.33) MUTATED                             0
  DEL PEAK 10(5P15.33) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 10(5P15.33) MUTATED                               0
  DEL PEAK 10(5P15.33) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 10(5P15.33) MUTATED                                            5
  DEL PEAK 10(5P15.33) WILD-TYPE                                         16
D35V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 10(5P15.33) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        8
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               11
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    1
  MYXOFIBROSARCOMA                                                                                    5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          5
                                                                          clus
vv                                                                         DEL PEAK 10(5P15.33) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         51
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 92
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      8
  MYXOFIBROSARCOMA                                                                                     19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 10(5P15.33) MUTATED    19   9   1   4
  DEL PEAK 10(5P15.33) WILD-TYPE 133  60   8  22
D35V7, multiclass
    clus
vv   DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  R0                           19                            133
  R1                            9                             60
  R2                            1                              8
  RX                            4                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5P15.33) MUTATED       1                         2    29
  DEL PEAK 10(5P15.33) WILD-TYPE     5                        16   195
D35V8, multiclass
                           clus
vv                          DEL PEAK 10(5P15.33) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               29
                           clus
vv                          DEL PEAK 10(5P15.33) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  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"
D35V9, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED     0  28
  DEL PEAK 10(5P15.33) WILD-TYPE   5 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED      0   28
  DEL PEAK 10(5P15.33) WILD-TYPE    5  192
                        clus
vv                       DEL PEAK 10(5P15.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 10(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 11(6P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P25.3) MUTATED    53  28
  DEL PEAK 11(6P25.3) WILD-TYPE 106  70
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           81                           176 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           28                            70 
$`DEL PEAK 11(6P25.3) MUTATED`
TCGA-DX-A6BK TCGA-DX-A7ET TCGA-DX-AB2X TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 
       16.18        15.22        13.28       101.98        37.02        12.62 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-VT-A80J 
       28.21        22.62         8.28        18.08       188.15        26.17 
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       68.55        44.91        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A3LT 
       36.03        26.56        45.11        18.54        74.66        49.05 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       33.44        44.68        10.68        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       85.45        45.99        24.26        52.77        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS 
       59.84        82.68        36.33        31.96         3.06        78.28 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BU 
      101.23        34.49        62.20        47.87        40.77        36.69 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       77.88       106.55        19.89        34.88         4.57        33.30 
TCGA-IE-A3OV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A6RV 
       80.48        37.12       171.09         1.05       101.26         5.19 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-PC-A5DL TCGA-QC-A7B5 
       16.41        35.28        25.41        19.73        37.55        13.08 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       18.08        37.12        16.77        18.94        22.82        25.35 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7W8 TCGA-X6-A8C3 
       10.72        84.79        38.27        65.46        26.43        19.17 
TCGA-X6-A8C5 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       50.86         4.37        15.98 

$`DEL PEAK 11(6P25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        67.20        34.36        75.32 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
      106.45        22.85        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-KF-A41W 
       16.60        52.11        26.93        52.27       159.29        11.70 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 
       17.75         6.35        20.94        17.52        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       50.01        19.69        53.49        88.57        54.74        25.25 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64         0.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
       95.38        79.17         9.04        86.83       136.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A48J 
       35.77        51.02         4.54        14.99        73.87         9.73 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BE 
       35.28        26.47        37.58        15.95        37.41        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       36.85        26.99        41.00        50.50        16.87        86.30 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       64.21        21.30        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR 
       20.05         9.34        61.97        45.14        38.17       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
        9.21        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N8 
       21.70        20.32        15.48         8.05        67.63         0.72 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
        9.80        19.53         3.22         1.38        19.89        25.22 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        85.97         5.92        16.41         3.91        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-LI-A67I 
       62.17       123.78        17.36        23.38        63.81        30.31 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        21.73        14.99        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
       10.45         7.36       122.96        38.63        81.01        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF 
        1.84        46.82        48.59        35.90       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B 
       64.77        10.52         0.72         3.88        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        12.46        11.93         4.80 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       30.84        35.18        20.65        29.46        27.32        36.43 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                         1.05                          0.49 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                        35.28                         29.21 
[1] "1.1 - 188.2 (35.3)" "0.5 - 159.3 (29.2)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 11(6P25.3) MUTATED                1                  1
  DEL PEAK 11(6P25.3) WILD-TYPE              0                  6
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 11(6P25.3) MUTATED                     0                   1
  DEL PEAK 11(6P25.3) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 11(6P25.3) MUTATED                               0
  DEL PEAK 11(6P25.3) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 11(6P25.3) MUTATED                       0                     10
  DEL PEAK 11(6P25.3) WILD-TYPE                     1                     18
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 11(6P25.3) MUTATED                      1                    0
  DEL PEAK 11(6P25.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 11(6P25.3) MUTATED                                       0
  DEL PEAK 11(6P25.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 11(6P25.3) MUTATED                                  0
  DEL PEAK 11(6P25.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 11(6P25.3) MUTATED                                                0
  DEL PEAK 11(6P25.3) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 11(6P25.3) MUTATED                                 3
  DEL PEAK 11(6P25.3) WILD-TYPE                               7
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 11(6P25.3) MUTATED                                         0
  DEL PEAK 11(6P25.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 11(6P25.3) MUTATED                              2
  DEL PEAK 11(6P25.3) WILD-TYPE                            2
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 11(6P25.3) MUTATED                         0
  DEL PEAK 11(6P25.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 11(6P25.3) MUTATED                                  8
  DEL PEAK 11(6P25.3) WILD-TYPE                                9
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 11(6P25.3) MUTATED                                         4
  DEL PEAK 11(6P25.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 11(6P25.3) MUTATED                              8
  DEL PEAK 11(6P25.3) WILD-TYPE                           36
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 11(6P25.3) MUTATED                                         1
  DEL PEAK 11(6P25.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 11(6P25.3) MUTATED                                           1
  DEL PEAK 11(6P25.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 11(6P25.3) MUTATED                                                  0
  DEL PEAK 11(6P25.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 11(6P25.3) MUTATED                                          3
  DEL PEAK 11(6P25.3) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 11(6P25.3) MUTATED                                                         0
  DEL PEAK 11(6P25.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 11(6P25.3) MUTATED                                            0
  DEL PEAK 11(6P25.3) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 11(6P25.3) MUTATED                                                  28
  DEL PEAK 11(6P25.3) WILD-TYPE                                                45
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 11(6P25.3) MUTATED                                                    2
  DEL PEAK 11(6P25.3) WILD-TYPE                                                  1
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 11(6P25.3) MUTATED                                    1
  DEL PEAK 11(6P25.3) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 11(6P25.3) MUTATED                          2
  DEL PEAK 11(6P25.3) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 11(6P25.3) MUTATED                             1
  DEL PEAK 11(6P25.3) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 11(6P25.3) MUTATED                           0
  DEL PEAK 11(6P25.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 11(6P25.3) MUTATED                                   1
  DEL PEAK 11(6P25.3) WILD-TYPE                                 6
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 11(6P25.3) MUTATED                                   1
  DEL PEAK 11(6P25.3) WILD-TYPE                                 4
D36V3, multiclass
                                                         clus
vv                                                        DEL PEAK 11(6P25.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                1
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           10
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      2
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                      8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 1
                                                         clus
vv                                                        DEL PEAK 11(6P25.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  6
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             18
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        2
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P25.3) MUTATED   45 36
  DEL PEAK 11(6P25.3) WILD-TYPE 94 82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     45   36
  DEL PEAK 11(6P25.3) WILD-TYPE   94   82
        clus
vv       DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  FEMALE                          45                            94
  MALE                            36                            82
[1] 2 2
[1] FALSE
D36V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED    56  23
  DEL PEAK 11(6P25.3) WILD-TYPE 123  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     56   23
  DEL PEAK 11(6P25.3) WILD-TYPE  123   49
     clus
vv    DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  NO                           56                           123
  YES                          23                            49
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 11(6P25.3) MUTATED                             11             1
  DEL PEAK 11(6P25.3) WILD-TYPE                           48             1
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 11(6P25.3) MUTATED                                                                          0
  DEL PEAK 11(6P25.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 11(6P25.3) MUTATED                     45
  DEL PEAK 11(6P25.3) WILD-TYPE                   58
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 11(6P25.3) MUTATED                                                  4
  DEL PEAK 11(6P25.3) WILD-TYPE                                                5
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 11(6P25.3) MUTATED                  7
  DEL PEAK 11(6P25.3) WILD-TYPE               17
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 11(6P25.3) MUTATED                                                          7
  DEL PEAK 11(6P25.3) WILD-TYPE                                                       21
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 11(6P25.3) MUTATED                                          0
  DEL PEAK 11(6P25.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 11(6P25.3) MUTATED                             0
  DEL PEAK 11(6P25.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 11(6P25.3) MUTATED                               0
  DEL PEAK 11(6P25.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 11(6P25.3) MUTATED                                            6
  DEL PEAK 11(6P25.3) WILD-TYPE                                         15
D36V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 11(6P25.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      11
  DESMOID TUMOR                                                                                      1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              45
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   4
  MYXOFIBROSARCOMA                                                                                   7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         6
                                                                          clus
vv                                                                         DEL PEAK 11(6P25.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        48
  DESMOID TUMOR                                                                                        1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                58
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                    17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          15
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(6P25.3) MUTATED    49  20   3   8
  DEL PEAK 11(6P25.3) WILD-TYPE 103  49   6  18
D36V7, multiclass
    clus
vv   DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  R0                          49                           103
  R1                          20                            49
  R2                           3                             6
  RX                           8                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6P25.3) MUTATED       2                         4    72
  DEL PEAK 11(6P25.3) WILD-TYPE     4                        14   152
D36V8, multiclass
                           clus
vv                          DEL PEAK 11(6P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              72
                           clus
vv                          DEL PEAK 11(6P25.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED     0  69
  DEL PEAK 11(6P25.3) WILD-TYPE   5 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED      0   69
  DEL PEAK 11(6P25.3) WILD-TYPE    5  151
                        clus
vv                       DEL PEAK 11(6P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK 11(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           151
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 12(6Q14.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6Q14.1) MUTATED    49  29
  DEL PEAK 12(6Q14.1) WILD-TYPE 110  69
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           78                           179 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           29                            69 
$`DEL PEAK 12(6Q14.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB32 TCGA-HB-A43Z TCGA-PC-A5DM 
       34.68        67.20        14.07       101.98        37.02         6.35 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
       20.94       188.15        26.17        19.69        88.57        44.91 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-DX-A1KY TCGA-DX-A1KZ 
       25.25        42.84        38.47        26.56        12.85        45.11 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF 
       33.44        44.68        51.02        14.99        10.68        85.45 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A6BA TCGA-DX-A6YR TCGA-DX-A6YS 
       45.99        24.26        46.03        82.68        41.00        78.28 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BL 
       16.87        64.21        21.30        34.49        62.20        45.14 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V 
       40.77       150.35        36.69        66.74        77.88       106.55 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       49.15        20.32        80.48         3.22        37.12        25.22 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT 
       16.41         1.05        62.17        23.38         5.19        16.41 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-QC-A7B5 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF 
       25.41        19.73        13.08        35.90        37.12       111.98 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-VT-A80G 
       10.52        16.77         3.88        22.82        25.35        10.72 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WB 
       11.93        84.79        65.46        22.62        26.43        18.08 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       45.34        19.17        20.65        50.86         4.37        15.98 

$`DEL PEAK 12(6Q14.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       17.95        14.43        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        12.62        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
      159.29        22.62        11.70        17.75         8.28        18.08 
TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        41.49        35.08        50.01        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       54.74        14.37        10.32        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        32.71        68.61        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
       79.17         9.04        49.05        86.83       136.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       35.77         4.54        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
        9.73        35.28        52.77        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        15.95        37.41        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 
       36.85        26.99         3.06        50.50        86.30       101.23 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       61.97        47.87        38.17        27.95        40.44        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        86.10         9.21        50.40        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        21.70        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI 
       34.88         4.57        33.30         0.72         9.80        19.53 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
        1.38        19.89       171.09        13.58        85.97         5.92 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS 
        3.91       101.26        53.33       123.78        17.36        63.81 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
       35.28        30.31         0.49        21.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71Q 
       48.59       130.32        64.77         0.72        18.94        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ 
        8.61        19.63        13.22        13.41        12.46         4.80 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       38.27         8.58        63.35        35.90        30.84        35.18 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43        13.38        15.95 

  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                         1.05                          0.49 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                       188.15                        171.09 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                       33.965                        30.840 
[1] "1.1 - 188.2 (34.0)" "0.5 - 171.1 (30.8)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 12(6Q14.1) MUTATED                1                  3
  DEL PEAK 12(6Q14.1) WILD-TYPE              0                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 12(6Q14.1) MUTATED                     0                   1
  DEL PEAK 12(6Q14.1) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 12(6Q14.1) MUTATED                               1
  DEL PEAK 12(6Q14.1) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 12(6Q14.1) MUTATED                       0                      3
  DEL PEAK 12(6Q14.1) WILD-TYPE                     1                     25
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 12(6Q14.1) MUTATED                      1                    0
  DEL PEAK 12(6Q14.1) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 12(6Q14.1) MUTATED                                       0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 12(6Q14.1) MUTATED                                  0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 12(6Q14.1) MUTATED                                                1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 12(6Q14.1) MUTATED                                 3
  DEL PEAK 12(6Q14.1) WILD-TYPE                               7
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 12(6Q14.1) MUTATED                                         0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 12(6Q14.1) MUTATED                              2
  DEL PEAK 12(6Q14.1) WILD-TYPE                            2
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 12(6Q14.1) MUTATED                         0
  DEL PEAK 12(6Q14.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 12(6Q14.1) MUTATED                                 10
  DEL PEAK 12(6Q14.1) WILD-TYPE                                7
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 12(6Q14.1) MUTATED                                         4
  DEL PEAK 12(6Q14.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 12(6Q14.1) MUTATED                             17
  DEL PEAK 12(6Q14.1) WILD-TYPE                           27
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 12(6Q14.1) MUTATED                                         1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 12(6Q14.1) MUTATED                                           1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 12(6Q14.1) MUTATED                                                  0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 12(6Q14.1) MUTATED                                          1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                        7
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 12(6Q14.1) MUTATED                                                         1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 12(6Q14.1) MUTATED                                            1
  DEL PEAK 12(6Q14.1) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 12(6Q14.1) MUTATED                                                  18
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                55
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 12(6Q14.1) MUTATED                                                    2
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                  1
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 12(6Q14.1) MUTATED                                    0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 12(6Q14.1) MUTATED                          2
  DEL PEAK 12(6Q14.1) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 12(6Q14.1) MUTATED                             1
  DEL PEAK 12(6Q14.1) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 12(6Q14.1) MUTATED                           0
  DEL PEAK 12(6Q14.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 12(6Q14.1) MUTATED                                   2
  DEL PEAK 12(6Q14.1) WILD-TYPE                                 5
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 12(6Q14.1) MUTATED                                   0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                 5
D37V3, multiclass
                                                         clus
vv                                                        DEL PEAK 12(6Q14.1) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                            3
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      2
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                 10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 0
                                                         clus
vv                                                        DEL PEAK 12(6Q14.1) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             25
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        2
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  55
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                               cls
clus                             0  1
  DEL PEAK 12(6Q14.1) MUTATED   43 35
  DEL PEAK 12(6Q14.1) WILD-TYPE 96 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q14.1) MUTATED     43   35
  DEL PEAK 12(6Q14.1) WILD-TYPE   96   83
        clus
vv       DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE
  FEMALE                          43                            96
  MALE                            35                            83
[1] 2 2
[1] FALSE
D37V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q14.1) MUTATED    46  30
  DEL PEAK 12(6Q14.1) WILD-TYPE 133  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q14.1) MUTATED     46   30
  DEL PEAK 12(6Q14.1) WILD-TYPE  133   42
     clus
vv    DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE
  NO                           46                           133
  YES                          30                            42
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 12(6Q14.1) MUTATED                             11             1
  DEL PEAK 12(6Q14.1) WILD-TYPE                           48             1
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 12(6Q14.1) MUTATED                                                                          0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 12(6Q14.1) MUTATED                     33
  DEL PEAK 12(6Q14.1) WILD-TYPE                   70
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 12(6Q14.1) MUTATED                                                  5
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                4
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 12(6Q14.1) MUTATED                 11
  DEL PEAK 12(6Q14.1) WILD-TYPE               13
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 12(6Q14.1) MUTATED                                                          9
  DEL PEAK 12(6Q14.1) WILD-TYPE                                                       19
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 12(6Q14.1) MUTATED                                          0
  DEL PEAK 12(6Q14.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 12(6Q14.1) MUTATED                             0
  DEL PEAK 12(6Q14.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 12(6Q14.1) MUTATED                               0
  DEL PEAK 12(6Q14.1) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 12(6Q14.1) MUTATED                                            8
  DEL PEAK 12(6Q14.1) WILD-TYPE                                         13
D37V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 12(6Q14.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      11
  DESMOID TUMOR                                                                                      1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              33
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   5
  MYXOFIBROSARCOMA                                                                                  11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
                                                                          clus
vv                                                                         DEL PEAK 12(6Q14.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        48
  DESMOID TUMOR                                                                                        1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                70
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     4
  MYXOFIBROSARCOMA                                                                                    13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(6Q14.1) MUTATED    45  23   2   7
  DEL PEAK 12(6Q14.1) WILD-TYPE 107  46   7  19
D37V7, multiclass
    clus
vv   DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE
  R0                          45                           107
  R1                          23                            46
  R2                           2                             7
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q14.1) MUTATED       1                         6    69
  DEL PEAK 12(6Q14.1) WILD-TYPE     5                        12   155
D37V8, multiclass
                           clus
vv                          DEL PEAK 12(6Q14.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              69
                           clus
vv                          DEL PEAK 12(6Q14.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q14.1) MUTATED     1  68
  DEL PEAK 12(6Q14.1) WILD-TYPE   4 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q14.1) MUTATED      1   68
  DEL PEAK 12(6Q14.1) WILD-TYPE    4  152
                        clus
vv                       DEL PEAK 12(6Q14.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 12(6Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           152
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    41  30
  DEL PEAK 13(7Q36.3) WILD-TYPE 118  68
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           71                           186 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           30                            68 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P 
       34.68        34.36        15.22        14.43        14.07        12.07 
TCGA-DX-AB2W TCGA-HB-A43Z TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-X6-A8C6 TCGA-3B-A9HQ 
      106.45        37.02        22.62        18.08        35.08        68.55 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L4 
       14.37        10.32        18.64        68.61        18.54        66.94 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48J 
       74.66         6.28        33.44        51.02        50.43         9.73 
TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ 
       35.28        46.03        26.47        31.96        26.99         3.06 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       78.28        21.30        30.35         9.34        45.14        47.87 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-HB-A3L4 
       40.44        36.69        60.66        17.79        66.74        34.88 
TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-K1-A42W 
        4.57         9.80        37.12        25.22         5.92        62.17 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VC 
       63.81        16.41        25.41        17.65        18.08        35.90 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QU 
      111.98        10.52        18.94        22.82         8.61        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
       10.72        12.46        84.79        38.27        65.46         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       63.35        26.43        35.18        19.17        20.65 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        75.32        17.95 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       15.85        40.60        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 
       60.00        84.66        32.15        16.60        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS 
       41.49        50.01        19.69        53.49        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       54.74        25.25        42.84        38.47        36.03        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
        0.56        14.04        32.71        12.85        45.11        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       85.02        33.53         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
        4.54        14.99        10.68        73.87        68.55        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V 
       85.45        45.99        24.26        52.77       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       36.85        41.00        50.50        16.87        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        34.49        62.20       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       20.05        61.97        38.17        40.77       150.35        27.95 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         6.58         1.15        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       86.10         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
       15.48         8.05        67.63        33.30         0.72        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA 
       19.53         3.22         1.38        19.89       171.09        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU TCGA-LI-A67I 
      123.78        17.36        23.38         5.19        35.28        30.31 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD 
       81.01        13.08         1.84        46.82        48.59        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P 
      130.32        64.77         0.72        16.77         3.88        25.35 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8Y0 
       32.75        19.63        13.22        11.93         4.80        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X6-A8C7 
       35.90        18.08        45.34        30.84        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         3.06                          0.49 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       111.98                        188.15 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       26.470                        32.005 
[1] "3.1 - 112.0 (26.5)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.3"
D38V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 13(7Q36.3) MUTATED                0                  2
  DEL PEAK 13(7Q36.3) WILD-TYPE              1                  5
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 13(7Q36.3) MUTATED                     0                   0
  DEL PEAK 13(7Q36.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 13(7Q36.3) MUTATED                               1
  DEL PEAK 13(7Q36.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 13(7Q36.3) MUTATED                       0                     11
  DEL PEAK 13(7Q36.3) WILD-TYPE                     1                     17
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 13(7Q36.3) MUTATED                      0                    0
  DEL PEAK 13(7Q36.3) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 13(7Q36.3) MUTATED                                       0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 13(7Q36.3) MUTATED                                  0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 13(7Q36.3) MUTATED                                                0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 13(7Q36.3) MUTATED                                 2
  DEL PEAK 13(7Q36.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 13(7Q36.3) MUTATED                                         0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 13(7Q36.3) MUTATED                              0
  DEL PEAK 13(7Q36.3) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 13(7Q36.3) MUTATED                         0
  DEL PEAK 13(7Q36.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 13(7Q36.3) MUTATED                                  7
  DEL PEAK 13(7Q36.3) WILD-TYPE                               10
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 13(7Q36.3) MUTATED                                         4
  DEL PEAK 13(7Q36.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 13(7Q36.3) MUTATED                             13
  DEL PEAK 13(7Q36.3) WILD-TYPE                           31
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 13(7Q36.3) MUTATED                                         0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 13(7Q36.3) MUTATED                                           1
  DEL PEAK 13(7Q36.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 13(7Q36.3) MUTATED                                                  0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 13(7Q36.3) MUTATED                                          2
  DEL PEAK 13(7Q36.3) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 13(7Q36.3) MUTATED                                                         0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 13(7Q36.3) MUTATED                                            1
  DEL PEAK 13(7Q36.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 13(7Q36.3) MUTATED                                                  18
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                55
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 13(7Q36.3) MUTATED                                                    1
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 13(7Q36.3) MUTATED                                    2
  DEL PEAK 13(7Q36.3) WILD-TYPE                                  0
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 13(7Q36.3) MUTATED                          0
  DEL PEAK 13(7Q36.3) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 13(7Q36.3) MUTATED                             1
  DEL PEAK 13(7Q36.3) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 13(7Q36.3) MUTATED                           0
  DEL PEAK 13(7Q36.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 13(7Q36.3) MUTATED                                   4
  DEL PEAK 13(7Q36.3) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 13(7Q36.3) MUTATED                                   1
  DEL PEAK 13(7Q36.3) WILD-TYPE                                 4
D38V3, multiclass
                                                         clus
vv                                                        DEL PEAK 13(7Q36.3) MUTATED
  CHEST - BREAST                                                                    0
  CHEST - CHEST WALL                                                                2
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           11
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                2
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 1
                                                         clus
vv                                                        DEL PEAK 13(7Q36.3) WILD-TYPE
  CHEST - BREAST                                                                      1
  CHEST - CHEST WALL                                                                  5
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             17
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       31
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  55
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  0
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    37  34
  DEL PEAK 13(7Q36.3) WILD-TYPE 102  84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     37   34
  DEL PEAK 13(7Q36.3) WILD-TYPE  102   84
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          37                           102
  MALE                            34                            84
[1] 2 2
[1] FALSE
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    46  24
  DEL PEAK 13(7Q36.3) WILD-TYPE 133  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     46   24
  DEL PEAK 13(7Q36.3) WILD-TYPE  133   48
     clus
vv    DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  NO                           46                           133
  YES                          24                            48
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 13(7Q36.3) MUTATED                             12             0
  DEL PEAK 13(7Q36.3) WILD-TYPE                           47             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 13(7Q36.3) MUTATED                                                                          0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 13(7Q36.3) MUTATED                     27
  DEL PEAK 13(7Q36.3) WILD-TYPE                   76
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 13(7Q36.3) MUTATED                                                  2
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 13(7Q36.3) MUTATED                  8
  DEL PEAK 13(7Q36.3) WILD-TYPE               16
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 13(7Q36.3) MUTATED                                                         13
  DEL PEAK 13(7Q36.3) WILD-TYPE                                                       15
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 13(7Q36.3) MUTATED                                          0
  DEL PEAK 13(7Q36.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 13(7Q36.3) MUTATED                             0
  DEL PEAK 13(7Q36.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 13(7Q36.3) MUTATED                               0
  DEL PEAK 13(7Q36.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 13(7Q36.3) MUTATED                                            9
  DEL PEAK 13(7Q36.3) WILD-TYPE                                         12
D38V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 13(7Q36.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      12
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                   8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         9
                                                                          clus
vv                                                                         DEL PEAK 13(7Q36.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        47
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(7Q36.3) MUTATED    40  21   0  10
  DEL PEAK 13(7Q36.3) WILD-TYPE 112  48   9  16
D38V7, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  R0                          40                           112
  R1                          21                            48
  R2                           0                             9
  RX                          10                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       3                         4    61
  DEL PEAK 13(7Q36.3) WILD-TYPE     3                        14   163
D38V8, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              61
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            14
  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"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED     1  63
  DEL PEAK 13(7Q36.3) WILD-TYPE   4 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED      1   63
  DEL PEAK 13(7Q36.3) WILD-TYPE    4  157
                        clus
vv                       DEL PEAK 13(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK 13(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           157
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED    45  36
  DEL PEAK 14(8P23.3) WILD-TYPE 114  62
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           81                           176 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           36                            62 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2P 
       31.53        16.18        34.36        15.22        17.95        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HB-A43Z TCGA-HS-A5N9 
      106.45        13.28       101.98        30.51        37.02        52.11 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
       17.75         6.35        35.08        19.69        88.57        44.91 
TCGA-3B-A9HV TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.37         0.56        32.71        68.61        45.11        18.54 
TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        6.28         9.04        49.05       136.44        44.68        31.86 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48K 
       51.02        10.68        73.87        50.43         9.73        45.99 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI 
       26.47        15.95         3.06        16.87        21.30        34.49 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       45.14        38.17        40.77        27.95        40.44        60.66 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V 
        1.15        17.79        12.00        86.10        77.88       106.55 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A6BZ 
       49.15        21.70        34.88         4.57         0.72        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A6RT TCGA-K1-A6RV 
       37.12       171.09        16.41         3.91        17.36         5.19 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q 
       21.73        19.73        48.59         3.88        22.82        32.75 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A7WC 
       13.41        10.72        12.46        84.79        26.43        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-Z4-AAPG 
       35.18        20.65        15.98 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        34.68        67.20        75.32        14.43        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       15.85        40.60        22.85        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       16.60        12.62        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        11.70         8.28        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        50.01        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 
       18.64        26.56        14.04        12.85        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC 
       86.83        33.44        35.77         4.54        14.99        68.55 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88        85.45        24.26        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN 
       50.50        86.30        64.21       101.23        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G 
       47.87       150.35        36.69        19.43         6.58        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        66.74         9.21        50.40        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        20.32        19.89        15.48         8.05        67.63 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         9.80        80.48        19.53         3.22         1.38 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN 
       25.22        13.58        85.97         5.92         1.05       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33        62.17       123.78        23.38        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J 
       35.28        30.31        25.41         0.49        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B 
       10.52         0.72        16.77        18.94        25.35         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY 
       19.63        13.22        11.93         4.80        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       22.62         8.58        63.35        35.90        18.08        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       171.09                        188.15 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       26.470                        32.725 
[1] "0.6 - 171.1 (26.5)" "0.5 - 188.2 (32.7)"
[1] "hr=" "1.5"
D39V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 14(8P23.3) MUTATED                1                  3
  DEL PEAK 14(8P23.3) WILD-TYPE              0                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 14(8P23.3) MUTATED                     0                   0
  DEL PEAK 14(8P23.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 14(8P23.3) MUTATED                               0
  DEL PEAK 14(8P23.3) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 14(8P23.3) MUTATED                       1                      7
  DEL PEAK 14(8P23.3) WILD-TYPE                     0                     21
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 14(8P23.3) MUTATED                      0                    0
  DEL PEAK 14(8P23.3) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 14(8P23.3) MUTATED                                       0
  DEL PEAK 14(8P23.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 14(8P23.3) MUTATED                                  0
  DEL PEAK 14(8P23.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 14(8P23.3) MUTATED                                                0
  DEL PEAK 14(8P23.3) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 14(8P23.3) MUTATED                                 2
  DEL PEAK 14(8P23.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 14(8P23.3) MUTATED                                         0
  DEL PEAK 14(8P23.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 14(8P23.3) MUTATED                              1
  DEL PEAK 14(8P23.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 14(8P23.3) MUTATED                         1
  DEL PEAK 14(8P23.3) WILD-TYPE                       1
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 14(8P23.3) MUTATED                                  7
  DEL PEAK 14(8P23.3) WILD-TYPE                               10
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 14(8P23.3) MUTATED                                         4
  DEL PEAK 14(8P23.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 14(8P23.3) MUTATED                             16
  DEL PEAK 14(8P23.3) WILD-TYPE                           28
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 14(8P23.3) MUTATED                                         0
  DEL PEAK 14(8P23.3) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 14(8P23.3) MUTATED                                           1
  DEL PEAK 14(8P23.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 14(8P23.3) MUTATED                                                  1
  DEL PEAK 14(8P23.3) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 14(8P23.3) MUTATED                                          3
  DEL PEAK 14(8P23.3) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 14(8P23.3) MUTATED                                                         1
  DEL PEAK 14(8P23.3) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 14(8P23.3) MUTATED                                            0
  DEL PEAK 14(8P23.3) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 14(8P23.3) MUTATED                                                  21
  DEL PEAK 14(8P23.3) WILD-TYPE                                                52
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 14(8P23.3) MUTATED                                                    1
  DEL PEAK 14(8P23.3) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 14(8P23.3) MUTATED                                    1
  DEL PEAK 14(8P23.3) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 14(8P23.3) MUTATED                          1
  DEL PEAK 14(8P23.3) WILD-TYPE                        4
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 14(8P23.3) MUTATED                             1
  DEL PEAK 14(8P23.3) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 14(8P23.3) MUTATED                           0
  DEL PEAK 14(8P23.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 14(8P23.3) MUTATED                                   5
  DEL PEAK 14(8P23.3) WILD-TYPE                                 2
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 14(8P23.3) MUTATED                                   2
  DEL PEAK 14(8P23.3) WILD-TYPE                                 3
D39V3, multiclass
                                                         clus
vv                                                        DEL PEAK 14(8P23.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                            7
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        DEL PEAK 14(8P23.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                             21
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  52
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   41 40
  DEL PEAK 14(8P23.3) WILD-TYPE 98 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     41   40
  DEL PEAK 14(8P23.3) WILD-TYPE   98   78
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          41                            98
  MALE                            40                            78
[1] 2 2
[1] FALSE
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    51  30
  DEL PEAK 14(8P23.3) WILD-TYPE 128  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     51   30
  DEL PEAK 14(8P23.3) WILD-TYPE  128   42
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                           51                           128
  YES                          30                            42
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 14(8P23.3) MUTATED                             20             0
  DEL PEAK 14(8P23.3) WILD-TYPE                           39             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 14(8P23.3) MUTATED                                                                          0
  DEL PEAK 14(8P23.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 14(8P23.3) MUTATED                     26
  DEL PEAK 14(8P23.3) WILD-TYPE                   77
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 14(8P23.3) MUTATED                                                  2
  DEL PEAK 14(8P23.3) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 14(8P23.3) MUTATED                 11
  DEL PEAK 14(8P23.3) WILD-TYPE               13
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 14(8P23.3) MUTATED                                                         14
  DEL PEAK 14(8P23.3) WILD-TYPE                                                       14
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 14(8P23.3) MUTATED                                          0
  DEL PEAK 14(8P23.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 14(8P23.3) MUTATED                             0
  DEL PEAK 14(8P23.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 14(8P23.3) MUTATED                               0
  DEL PEAK 14(8P23.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 14(8P23.3) MUTATED                                            8
  DEL PEAK 14(8P23.3) WILD-TYPE                                         13
D39V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 14(8P23.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      20
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              26
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                  11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         8
                                                                          clus
vv                                                                         DEL PEAK 14(8P23.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        39
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                77
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(8P23.3) MUTATED    47  24   5   5
  DEL PEAK 14(8P23.3) WILD-TYPE 105  45   4  21
D39V7, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  R0                          47                           105
  R1                          24                            45
  R2                           5                             4
  RX                           5                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED       1                         7    68
  DEL PEAK 14(8P23.3) WILD-TYPE     5                        11   156
D39V8, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              68
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            11
  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"
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     1  67
  DEL PEAK 14(8P23.3) WILD-TYPE   4 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      1   67
  DEL PEAK 14(8P23.3) WILD-TYPE    4  153
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           153
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 15(9P24.3) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P24.3) MUTATED    56  44
  DEL PEAK 15(9P24.3) WILD-TYPE 103  54
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                          100                           157 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                           44                            54 
$`DEL PEAK 15(9P24.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J 
       34.68        16.18        75.32        14.43        14.07        40.60 
TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB3A TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 
       12.07       101.98        32.15        22.62        11.70         8.28 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
       20.94       188.15        26.17        19.69        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       54.74        14.37        38.47        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23V TCGA-DX-A23Y 
       14.04        45.11        54.21        85.02        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       27.81         9.04        49.05       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       31.86        51.02        10.68        85.45         9.73        45.99 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       59.84        37.58        82.68        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        16.87        86.30        64.21        21.30        34.49 
TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       30.35        29.49         9.34        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-FX-A2QS TCGA-FX-A3RE 
      150.35        40.44         6.58        17.79        49.15        21.70 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 
       67.63         0.72        19.53         3.22       171.09         5.92 
TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 
        3.91        62.17        23.38        63.81        16.41        25.41 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       19.73        10.45         7.36        38.63        81.01        13.08 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
       18.08        35.90        10.52        16.77        25.35        32.75 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        8.61        10.72        84.79        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WC TCGA-X9-A971 TCGA-Z4-AAPG 
       63.35        45.34        27.32        15.98 

$`DEL PEAK 15(9P24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        67.20        34.36        15.22        17.95 
TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       15.85       106.45        13.28        22.85        30.51        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       84.66        16.60        37.02        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       52.27        28.21       159.29        17.75         6.35        18.08 
TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        41.49        35.08        50.01        53.49        68.55 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX 
       25.25        42.84        10.32        36.03        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       12.85        18.54        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       76.41        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       86.83        35.77         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       50.43        34.88        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47       108.82        15.95        37.41        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO 
       36.85        26.99        50.50       101.23        62.20       152.12 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BS TCGA-DX-A8BU 
       48.20        20.05        61.97        45.14        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43         1.15        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31        31.13        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
        8.05        34.88         4.57        33.30         9.80        80.48 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        19.89        37.12        25.22        13.58        85.97 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         1.05       101.26        53.33       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
        5.19        35.28        30.31         0.49        21.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QC-AA9N 
       17.98        22.39        11.57       122.96        37.55        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
        1.84        46.82        48.59        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8C 
       64.77         0.72        18.94         3.88        22.82        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WP-A9GB 
       13.22        13.41        12.46        11.93         4.80         8.58 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       26.43        35.90        18.08        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                       31.105                        31.130 
[1] "0.6 - 188.2 (31.1)" "0.5 - 159.3 (31.1)"
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 15(9P24.3) MUTATED                1                  5
  DEL PEAK 15(9P24.3) WILD-TYPE              0                  2
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 15(9P24.3) MUTATED                     0                   1
  DEL PEAK 15(9P24.3) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 15(9P24.3) MUTATED                               1
  DEL PEAK 15(9P24.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 15(9P24.3) MUTATED                       1                     12
  DEL PEAK 15(9P24.3) WILD-TYPE                     0                     16
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 15(9P24.3) MUTATED                      1                    0
  DEL PEAK 15(9P24.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 15(9P24.3) MUTATED                                       1
  DEL PEAK 15(9P24.3) WILD-TYPE                                     1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 15(9P24.3) MUTATED                                  0
  DEL PEAK 15(9P24.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 15(9P24.3) MUTATED                                                0
  DEL PEAK 15(9P24.3) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 15(9P24.3) MUTATED                                 2
  DEL PEAK 15(9P24.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 15(9P24.3) MUTATED                                         0
  DEL PEAK 15(9P24.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 15(9P24.3) MUTATED                              1
  DEL PEAK 15(9P24.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 15(9P24.3) MUTATED                         0
  DEL PEAK 15(9P24.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 15(9P24.3) MUTATED                                  5
  DEL PEAK 15(9P24.3) WILD-TYPE                               12
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 15(9P24.3) MUTATED                                         3
  DEL PEAK 15(9P24.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 15(9P24.3) MUTATED                             19
  DEL PEAK 15(9P24.3) WILD-TYPE                           25
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 15(9P24.3) MUTATED                                         1
  DEL PEAK 15(9P24.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 15(9P24.3) MUTATED                                           1
  DEL PEAK 15(9P24.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 15(9P24.3) MUTATED                                                  1
  DEL PEAK 15(9P24.3) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 15(9P24.3) MUTATED                                          0
  DEL PEAK 15(9P24.3) WILD-TYPE                                        8
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 15(9P24.3) MUTATED                                                         2
  DEL PEAK 15(9P24.3) WILD-TYPE                                                       0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 15(9P24.3) MUTATED                                            1
  DEL PEAK 15(9P24.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 15(9P24.3) MUTATED                                                  30
  DEL PEAK 15(9P24.3) WILD-TYPE                                                43
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 15(9P24.3) MUTATED                                                    1
  DEL PEAK 15(9P24.3) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 15(9P24.3) MUTATED                                    1
  DEL PEAK 15(9P24.3) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 15(9P24.3) MUTATED                          1
  DEL PEAK 15(9P24.3) WILD-TYPE                        4
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 15(9P24.3) MUTATED                             2
  DEL PEAK 15(9P24.3) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 15(9P24.3) MUTATED                           0
  DEL PEAK 15(9P24.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 15(9P24.3) MUTATED                                   4
  DEL PEAK 15(9P24.3) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 15(9P24.3) MUTATED                                   1
  DEL PEAK 15(9P24.3) WILD-TYPE                                 4
D40V3, multiclass
                                                         clus
vv                                                        DEL PEAK 15(9P24.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                5
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           12
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                30
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 1
                                                         clus
vv                                                        DEL PEAK 15(9P24.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                             16
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  43
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P24.3) MUTATED   57 43
  DEL PEAK 15(9P24.3) WILD-TYPE 82 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P24.3) MUTATED     57   43
  DEL PEAK 15(9P24.3) WILD-TYPE   82   75
        clus
vv       DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE
  FEMALE                          57                            82
  MALE                            43                            75
[1] 2 2
[1] FALSE
D40V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P24.3) MUTATED    68  30
  DEL PEAK 15(9P24.3) WILD-TYPE 111  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P24.3) MUTATED     68   30
  DEL PEAK 15(9P24.3) WILD-TYPE  111   42
     clus
vv    DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE
  NO                           68                           111
  YES                          30                            42
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 15(9P24.3) MUTATED                             22             0
  DEL PEAK 15(9P24.3) WILD-TYPE                           37             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 15(9P24.3) MUTATED                                                                          0
  DEL PEAK 15(9P24.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 15(9P24.3) MUTATED                     41
  DEL PEAK 15(9P24.3) WILD-TYPE                   62
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 15(9P24.3) MUTATED                                                  5
  DEL PEAK 15(9P24.3) WILD-TYPE                                                4
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 15(9P24.3) MUTATED                  9
  DEL PEAK 15(9P24.3) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 15(9P24.3) MUTATED                                                         13
  DEL PEAK 15(9P24.3) WILD-TYPE                                                       15
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 15(9P24.3) MUTATED                                          0
  DEL PEAK 15(9P24.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 15(9P24.3) MUTATED                             0
  DEL PEAK 15(9P24.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 15(9P24.3) MUTATED                               1
  DEL PEAK 15(9P24.3) WILD-TYPE                             5
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 15(9P24.3) MUTATED                                            9
  DEL PEAK 15(9P24.3) WILD-TYPE                                         12
D40V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 15(9P24.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      22
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              41
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   5
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         9
                                                                          clus
vv                                                                         DEL PEAK 15(9P24.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        37
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                62
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     4
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(9P24.3) MUTATED   55 28  5 11
  DEL PEAK 15(9P24.3) WILD-TYPE 97 41  4 15
D40V7, multiclass
    clus
vv   DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE
  R0                          55                            97
  R1                          28                            41
  R2                           5                             4
  RX                          11                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P24.3) MUTATED       2                         7    86
  DEL PEAK 15(9P24.3) WILD-TYPE     4                        11   138
D40V8, multiclass
                           clus
vv                          DEL PEAK 15(9P24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              86
                           clus
vv                          DEL PEAK 15(9P24.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P24.3) MUTATED     1  83
  DEL PEAK 15(9P24.3) WILD-TYPE   4 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P24.3) MUTATED      1   83
  DEL PEAK 15(9P24.3) WILD-TYPE    4  137
                        clus
vv                       DEL PEAK 15(9P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK 15(9P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           137
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(9P21.3) MUTATED   61 53
  DEL PEAK 16(9P21.3) WILD-TYPE 98 45
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          114                           143 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           53                            45 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J 
       34.68        16.18        75.32        14.43        14.07        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3A 
       12.07       106.45        13.28        22.85       101.98        32.15 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        11.70        17.75         8.28        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
       17.52        26.17        35.08        19.69        88.57        44.91 
TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       38.47        18.64        26.56         0.56        14.04        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R 
       12.85        45.11        18.54        54.21        85.02        74.66 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       66.87         6.28         9.04       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF 
       31.86        51.02         4.54        10.68        50.43        85.45 
TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF 
        9.73        26.47        59.84        37.58        82.68        31.96 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        41.00        78.28        16.87        86.30        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A8BJ TCGA-DX-A8BN 
       21.30        34.49        30.35        29.49         9.34        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       40.77       150.35        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       12.00        66.74        49.15        21.70        19.89        67.63 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-K1-A42W 
        0.72        19.53         3.22       171.09         5.92        62.17 
TCGA-K1-A6RU TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA 
       23.38        63.81        25.41        19.73        10.45         7.36 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       38.63        81.01        13.08        18.08        48.59        35.90 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       64.77        10.52        16.77        25.35        32.75        19.63 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       13.41        10.72        12.46        38.27        65.46        22.62 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPG 
       45.34        19.17        20.65        27.32        36.43        15.98 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        67.20        34.36        15.22        17.95 
TCGA-DX-AB2H TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z 
       15.85        30.51        60.00        84.66        16.60        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       12.62        52.11        26.93        52.27        28.21       159.29 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ 
        6.35        18.08        41.49        50.01        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 
       54.74        25.25        14.37        42.84        10.32        36.03 
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
       32.71        33.53        66.94         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        95.38        79.17        49.05 
TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       86.83        35.77        14.99        73.87        68.55        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       45.99        24.26        35.28        52.77        46.03       108.82 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       15.95        37.41        36.33        28.96        36.85        26.99 
TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7ER TCGA-DX-A7ES 
       50.50       101.23        62.20       152.12        48.20        20.05 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       61.97        45.14        47.87        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
       60.66        15.72        65.98        86.10         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO 
      106.55        50.40        50.89        71.31        31.13        20.32 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA 
       15.48         8.05        34.88         4.57        33.30         9.80 
TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
       80.48         1.38        19.89        37.12        25.22        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
      123.78        17.36         5.19        16.41        35.28        30.31 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        21.73        14.99        17.98        22.39        11.57 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD 
      122.96        37.55        17.65         1.84        46.82        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
      130.32       111.98         0.72        18.94         3.88        22.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WP-A9GB 
        8.61        13.22        11.93         4.80        84.79         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       50.86        29.46         4.37        13.38        15.95 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                        26.32                         34.36 
[1] "0.6 - 188.2 (26.3)" "0.5 - 159.3 (34.4)"
[1] "hr=" "1.6"
D41V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 16(9P21.3) MUTATED                1                  5
  DEL PEAK 16(9P21.3) WILD-TYPE              0                  2
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 16(9P21.3) MUTATED                     0                   1
  DEL PEAK 16(9P21.3) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 16(9P21.3) MUTATED                               1
  DEL PEAK 16(9P21.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 16(9P21.3) MUTATED                       1                      9
  DEL PEAK 16(9P21.3) WILD-TYPE                     0                     19
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 16(9P21.3) MUTATED                      1                    0
  DEL PEAK 16(9P21.3) WILD-TYPE                    1                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 16(9P21.3) MUTATED                                       0
  DEL PEAK 16(9P21.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 16(9P21.3) MUTATED                                  0
  DEL PEAK 16(9P21.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 16(9P21.3) MUTATED                                                0
  DEL PEAK 16(9P21.3) WILD-TYPE                                              2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 16(9P21.3) MUTATED                                 4
  DEL PEAK 16(9P21.3) WILD-TYPE                               6
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 16(9P21.3) MUTATED                                         1
  DEL PEAK 16(9P21.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 16(9P21.3) MUTATED                              1
  DEL PEAK 16(9P21.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 16(9P21.3) MUTATED                         1
  DEL PEAK 16(9P21.3) WILD-TYPE                       1
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 16(9P21.3) MUTATED                                  9
  DEL PEAK 16(9P21.3) WILD-TYPE                                8
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 16(9P21.3) MUTATED                                         3
  DEL PEAK 16(9P21.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 16(9P21.3) MUTATED                             21
  DEL PEAK 16(9P21.3) WILD-TYPE                           23
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 16(9P21.3) MUTATED                                         1
  DEL PEAK 16(9P21.3) WILD-TYPE                                       3
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 16(9P21.3) MUTATED                                           0
  DEL PEAK 16(9P21.3) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 16(9P21.3) MUTATED                                                  1
  DEL PEAK 16(9P21.3) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 16(9P21.3) MUTATED                                          1
  DEL PEAK 16(9P21.3) WILD-TYPE                                        7
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 16(9P21.3) MUTATED                                                         2
  DEL PEAK 16(9P21.3) WILD-TYPE                                                       0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 16(9P21.3) MUTATED                                            1
  DEL PEAK 16(9P21.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 16(9P21.3) MUTATED                                                  36
  DEL PEAK 16(9P21.3) WILD-TYPE                                                37
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 16(9P21.3) MUTATED                                                    1
  DEL PEAK 16(9P21.3) WILD-TYPE                                                  2
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 16(9P21.3) MUTATED                                    1
  DEL PEAK 16(9P21.3) WILD-TYPE                                  1
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 16(9P21.3) MUTATED                          2
  DEL PEAK 16(9P21.3) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 16(9P21.3) MUTATED                             2
  DEL PEAK 16(9P21.3) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 16(9P21.3) MUTATED                           0
  DEL PEAK 16(9P21.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 16(9P21.3) MUTATED                                   4
  DEL PEAK 16(9P21.3) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 16(9P21.3) MUTATED                                   2
  DEL PEAK 16(9P21.3) WILD-TYPE                                 3
D41V3, multiclass
                                                         clus
vv                                                        DEL PEAK 16(9P21.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                5
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                            9
  HEAD AND NECK - HEAD                                                              1
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                36
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                1
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        DEL PEAK 16(9P21.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                             19
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  37
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                               cls
clus                             0  1
  DEL PEAK 16(9P21.3) MUTATED   64 50
  DEL PEAK 16(9P21.3) WILD-TYPE 75 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     64   50
  DEL PEAK 16(9P21.3) WILD-TYPE   75   68
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          64                            75
  MALE                            50                            68
[1] 2 2
[1] FALSE
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    77  36
  DEL PEAK 16(9P21.3) WILD-TYPE 102  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     77   36
  DEL PEAK 16(9P21.3) WILD-TYPE  102   36
     clus
vv    DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  NO                           77                           102
  YES                          36                            36
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 16(9P21.3) MUTATED                             25             0
  DEL PEAK 16(9P21.3) WILD-TYPE                           34             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 16(9P21.3) MUTATED                                                                          0
  DEL PEAK 16(9P21.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 16(9P21.3) MUTATED                     39
  DEL PEAK 16(9P21.3) WILD-TYPE                   64
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 16(9P21.3) MUTATED                                                  7
  DEL PEAK 16(9P21.3) WILD-TYPE                                                2
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 16(9P21.3) MUTATED                 12
  DEL PEAK 16(9P21.3) WILD-TYPE               12
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 16(9P21.3) MUTATED                                                         17
  DEL PEAK 16(9P21.3) WILD-TYPE                                                       11
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 16(9P21.3) MUTATED                                          0
  DEL PEAK 16(9P21.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 16(9P21.3) MUTATED                             0
  DEL PEAK 16(9P21.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 16(9P21.3) MUTATED                               1
  DEL PEAK 16(9P21.3) WILD-TYPE                             5
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 16(9P21.3) MUTATED                                           13
  DEL PEAK 16(9P21.3) WILD-TYPE                                          8
D41V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 16(9P21.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      25
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              39
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   7
  MYXOFIBROSARCOMA                                                                                  12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        13
                                                                          clus
vv                                                                         DEL PEAK 16(9P21.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        34
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                64
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     2
  MYXOFIBROSARCOMA                                                                                    12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 16(9P21.3) MUTATED   60 36  5 12
  DEL PEAK 16(9P21.3) WILD-TYPE 92 33  4 14
D41V7, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  R0                          60                            92
  R1                          36                            33
  R2                           5                             4
  RX                          12                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED       4                         7    98
  DEL PEAK 16(9P21.3) WILD-TYPE     2                        11   126
D41V8, multiclass
                           clus
vv                          DEL PEAK 16(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              98
                           clus
vv                          DEL PEAK 16(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     2  95
  DEL PEAK 16(9P21.3) WILD-TYPE   3 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      2   95
  DEL PEAK 16(9P21.3) WILD-TYPE    3  125
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           125
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 17(9Q34.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9Q34.3) MUTATED    33  28
  DEL PEAK 17(9Q34.3) WILD-TYPE 126  70
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           61                           196 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           28                            70 
$`DEL PEAK 17(9Q34.3) MUTATED`
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-AB2W TCGA-DX-AB32 TCGA-IE-A4EH TCGA-LI-A9QH 
       67.20        34.36       106.45       101.98        26.93        17.75 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3B-A9I3 
        6.35        20.94       188.15        88.57        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A3M1 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J 
        0.56        14.04        44.68        68.55        50.43         9.73 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       26.47        59.84        15.95         3.06        41.00        78.28 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E 
       16.87        64.21        62.20        27.95        36.69        17.79 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       20.32        19.89        67.63         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
        9.80        80.48        25.22        13.58         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QU 
        1.05         3.91        62.17       123.78         5.19        35.28 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DO TCGA-SI-A71Q 
       25.41        19.73        14.99        10.45        81.01        32.75 
TCGA-VT-A80G TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 
       10.72        38.27         8.58        35.90        18.08        35.18 
TCGA-X9-A971 
       27.32 

$`DEL PEAK 17(9Q34.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        16.18        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        12.62        52.11        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-SG-A849 
      159.29        22.62        11.70         8.28        18.08        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
       26.17        41.49        35.08        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       68.55        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       10.32        38.47        36.03        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        33.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE 
       51.02         4.54        14.99        10.68        73.87        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       85.45        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
      108.82        37.58        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 
       31.96        36.85        26.99        50.50        86.30       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       40.77       150.35        40.44        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
        1.15        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       49.15        31.13        21.70        15.48         8.05        34.88 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
       19.53         3.22         1.38        19.89        37.12       171.09 
TCGA-IW-A3M4 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS 
       85.97       101.26        53.33        17.36        23.38        63.81 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
       16.41        30.31         0.49        21.73        17.98        22.39 
TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 
       11.57         7.36       122.96        37.55        38.63        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
       16.77        18.94         3.88        22.82        25.35         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC 
       84.79        65.46        22.62        63.35        26.43        45.34 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       30.84        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                       188.15                        171.09 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                        26.47                         32.43 
[1] "0.6 - 188.2 (26.5)" "0.5 - 171.1 (32.4)"
[1] "hr=" "1.4"
D42V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 17(9Q34.3) MUTATED                1                  4
  DEL PEAK 17(9Q34.3) WILD-TYPE              0                  3
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 17(9Q34.3) MUTATED                     0                   0
  DEL PEAK 17(9Q34.3) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 17(9Q34.3) MUTATED                               1
  DEL PEAK 17(9Q34.3) WILD-TYPE                             1
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 17(9Q34.3) MUTATED                       0                     12
  DEL PEAK 17(9Q34.3) WILD-TYPE                     1                     16
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 17(9Q34.3) MUTATED                      0                    0
  DEL PEAK 17(9Q34.3) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 17(9Q34.3) MUTATED                                       0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 17(9Q34.3) MUTATED                                  0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 17(9Q34.3) MUTATED                                                1
  DEL PEAK 17(9Q34.3) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 17(9Q34.3) MUTATED                                 2
  DEL PEAK 17(9Q34.3) WILD-TYPE                               8
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 17(9Q34.3) MUTATED                                         0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 17(9Q34.3) MUTATED                              0
  DEL PEAK 17(9Q34.3) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 17(9Q34.3) MUTATED                         0
  DEL PEAK 17(9Q34.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 17(9Q34.3) MUTATED                                  4
  DEL PEAK 17(9Q34.3) WILD-TYPE                               13
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 17(9Q34.3) MUTATED                                         4
  DEL PEAK 17(9Q34.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 17(9Q34.3) MUTATED                             10
  DEL PEAK 17(9Q34.3) WILD-TYPE                           34
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 17(9Q34.3) MUTATED                                         0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                       4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 17(9Q34.3) MUTATED                                           0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 17(9Q34.3) MUTATED                                                  1
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 17(9Q34.3) MUTATED                                          2
  DEL PEAK 17(9Q34.3) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 17(9Q34.3) MUTATED                                                         0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 17(9Q34.3) MUTATED                                            1
  DEL PEAK 17(9Q34.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 17(9Q34.3) MUTATED                                                  13
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                60
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 17(9Q34.3) MUTATED                                                    0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                  3
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 17(9Q34.3) MUTATED                                    0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 17(9Q34.3) MUTATED                          1
  DEL PEAK 17(9Q34.3) WILD-TYPE                        4
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 17(9Q34.3) MUTATED                             1
  DEL PEAK 17(9Q34.3) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 17(9Q34.3) MUTATED                           0
  DEL PEAK 17(9Q34.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 17(9Q34.3) MUTATED                                   3
  DEL PEAK 17(9Q34.3) WILD-TYPE                                 4
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 17(9Q34.3) MUTATED                                   0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                 5
D42V3, multiclass
                                                         clus
vv                                                        DEL PEAK 17(9Q34.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                4
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     1
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           12
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           0
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 0
                                                         clus
vv                                                        DEL PEAK 17(9Q34.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             16
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             2
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q34.3) MUTATED    36  25
  DEL PEAK 17(9Q34.3) WILD-TYPE 103  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED     36   25
  DEL PEAK 17(9Q34.3) WILD-TYPE  103   93
        clus
vv       DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                          36                           103
  MALE                            25                            93
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q34.3) MUTATED    39  22
  DEL PEAK 17(9Q34.3) WILD-TYPE 140  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED     39   22
  DEL PEAK 17(9Q34.3) WILD-TYPE  140   50
     clus
vv    DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE
  NO                           39                           140
  YES                          22                            50
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 17(9Q34.3) MUTATED                              3             0
  DEL PEAK 17(9Q34.3) WILD-TYPE                           56             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 17(9Q34.3) MUTATED                                                                          0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 17(9Q34.3) MUTATED                     36
  DEL PEAK 17(9Q34.3) WILD-TYPE                   67
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 17(9Q34.3) MUTATED                                                  2
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                7
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 17(9Q34.3) MUTATED                  9
  DEL PEAK 17(9Q34.3) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 17(9Q34.3) MUTATED                                                          5
  DEL PEAK 17(9Q34.3) WILD-TYPE                                                       23
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 17(9Q34.3) MUTATED                                          0
  DEL PEAK 17(9Q34.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 17(9Q34.3) MUTATED                             0
  DEL PEAK 17(9Q34.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 17(9Q34.3) MUTATED                               0
  DEL PEAK 17(9Q34.3) WILD-TYPE                             6
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 17(9Q34.3) MUTATED                                            6
  DEL PEAK 17(9Q34.3) WILD-TYPE                                         15
D42V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 17(9Q34.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       3
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              36
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   2
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         6
                                                                          clus
vv                                                                         DEL PEAK 17(9Q34.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        56
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                67
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     7
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            23
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          15
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(9Q34.3) MUTATED    37  12   7   5
  DEL PEAK 17(9Q34.3) WILD-TYPE 115  57   2  21
D42V7, multiclass
    clus
vv   DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE
  R0                          37                           115
  R1                          12                            57
  R2                           7                             2
  RX                           5                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9Q34.3) MUTATED       1                         9    45
  DEL PEAK 17(9Q34.3) WILD-TYPE     5                         9   179
D42V8, multiclass
                           clus
vv                          DEL PEAK 17(9Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                              45
                           clus
vv                          DEL PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q34.3) MUTATED     1  45
  DEL PEAK 17(9Q34.3) WILD-TYPE   4 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED      1   45
  DEL PEAK 17(9Q34.3) WILD-TYPE    4  175
                        clus
vv                       DEL PEAK 17(9Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK 17(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           175
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10P15.3) MUTATED   81 47
  DEL PEAK 18(10P15.3) WILD-TYPE 78 51
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           128                            129 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            47                             51 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.18        34.36        75.32        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IF-A4AK 
       12.07        22.85       101.98        37.02        12.62        52.27 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       22.62        11.70         6.35        20.94       188.15        17.52 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW 
       44.91        14.37        10.32        36.03        26.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LW 
       68.61        18.54        85.02        74.66         6.28       136.44 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       33.44        31.86        10.68        50.43        34.88        85.45 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 
       45.99        35.28        46.03        26.47        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       37.41        82.68        36.33         3.06        41.00        78.28 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BJ 
       16.87        64.21       101.23        62.20        30.35         9.34 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       47.87        40.77        27.95        40.44        60.66         6.58 
TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3C TCGA-FX-A2QS 
       12.00        86.10       106.55        50.40        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       21.70        20.32        67.63         4.57        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
       80.48        19.53         3.22        19.89        25.22       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU 
        5.92        16.41         3.91       101.26        62.17        23.38 
TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL 
        5.19        16.41        35.28        25.41         0.49        19.73 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
       14.99        10.45         7.36       122.96        37.55        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       13.08        17.65        46.82        48.59        35.90        37.12 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       10.52         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS 
       19.63        13.41        10.72        12.46        11.93        84.79 
TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
        8.58        45.34        30.84        19.17        20.65        50.86 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        34.68        67.20        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       40.60       106.45        13.28        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       32.15        16.60        52.11        26.93        28.21       159.29 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HT 
       17.75         8.28        18.08        26.17        41.49        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       25.25        42.84        38.47        18.64         0.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        45.11        54.21        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M1 
       95.38        79.17         9.04        49.05        86.83        44.68 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BE 
        9.73        24.26        52.77       108.82        59.84        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF 
       31.96        36.85        26.99        50.50        86.30        21.30 
TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       34.49       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
       45.14        38.17       150.35        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       17.79        15.72        65.98        66.74         9.21        77.88 
TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       50.89        31.13        19.89        15.48         8.05        34.88 
TCGA-HS-A5NA TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF 
        9.80         1.38        37.12        13.58        85.97         1.05 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS TCGA-LI-A67I TCGA-MB-A8JK 
       53.33       123.78        17.36        63.81        30.31        21.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       17.98        22.39        11.57        38.63         1.84        18.08 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32       111.98        64.77         0.72        16.77        18.94 
TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       13.22         4.80        38.27        65.46        22.62        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C7 TCGA-X9-A973 
       26.43        35.90        18.08        35.18        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                          0.49                           0.56 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                         29.15                          31.96 
[1] "0.5 - 188.2 (29.1)" "0.6 - 159.3 (32.0)"
[1] "hr=" "1"  
D43V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 18(10P15.3) MUTATED                1                  5
  DEL PEAK 18(10P15.3) WILD-TYPE              0                  2
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 18(10P15.3) MUTATED                     0                   0
  DEL PEAK 18(10P15.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 18(10P15.3) MUTATED                               1
  DEL PEAK 18(10P15.3) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 18(10P15.3) MUTATED                       1                     13
  DEL PEAK 18(10P15.3) WILD-TYPE                     0                     15
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 18(10P15.3) MUTATED                      1                    0
  DEL PEAK 18(10P15.3) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 18(10P15.3) MUTATED                                       0
  DEL PEAK 18(10P15.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 18(10P15.3) MUTATED                                  0
  DEL PEAK 18(10P15.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 18(10P15.3) MUTATED                                                1
  DEL PEAK 18(10P15.3) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 18(10P15.3) MUTATED                                 4
  DEL PEAK 18(10P15.3) WILD-TYPE                               6
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 18(10P15.3) MUTATED                                         0
  DEL PEAK 18(10P15.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 18(10P15.3) MUTATED                              2
  DEL PEAK 18(10P15.3) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 18(10P15.3) MUTATED                         1
  DEL PEAK 18(10P15.3) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 18(10P15.3) MUTATED                                  8
  DEL PEAK 18(10P15.3) WILD-TYPE                                9
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 18(10P15.3) MUTATED                                         5
  DEL PEAK 18(10P15.3) WILD-TYPE                                       0
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 18(10P15.3) MUTATED                             23
  DEL PEAK 18(10P15.3) WILD-TYPE                           21
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 18(10P15.3) MUTATED                                         3
  DEL PEAK 18(10P15.3) WILD-TYPE                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 18(10P15.3) MUTATED                                           1
  DEL PEAK 18(10P15.3) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 18(10P15.3) MUTATED                                                  1
  DEL PEAK 18(10P15.3) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 18(10P15.3) MUTATED                                          4
  DEL PEAK 18(10P15.3) WILD-TYPE                                        4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 18(10P15.3) MUTATED                                                         2
  DEL PEAK 18(10P15.3) WILD-TYPE                                                       0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 18(10P15.3) MUTATED                                            1
  DEL PEAK 18(10P15.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 18(10P15.3) MUTATED                                                  32
  DEL PEAK 18(10P15.3) WILD-TYPE                                                41
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 18(10P15.3) MUTATED                                                    1
  DEL PEAK 18(10P15.3) WILD-TYPE                                                  2
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 18(10P15.3) MUTATED                                    2
  DEL PEAK 18(10P15.3) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 18(10P15.3) MUTATED                          3
  DEL PEAK 18(10P15.3) WILD-TYPE                        2
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 18(10P15.3) MUTATED                             4
  DEL PEAK 18(10P15.3) WILD-TYPE                           0
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 18(10P15.3) MUTATED                           0
  DEL PEAK 18(10P15.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 18(10P15.3) MUTATED                                   4
  DEL PEAK 18(10P15.3) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 18(10P15.3) MUTATED                                   3
  DEL PEAK 18(10P15.3) WILD-TYPE                                 2
D43V3, multiclass
                                                         clus
vv                                                        DEL PEAK 18(10P15.3) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 5
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            13
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            5
  LOWER EXTREMITY - THIGH/KNEE                                                      23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 32
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           3
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        DEL PEAK 18(10P15.3) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   2
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              15
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              0
  LOWER EXTREMITY - THIGH/KNEE                                                        21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   41
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             2
  SUPERFICIAL TRUNK - BUTTOCK                                                          0
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   76 52
  DEL PEAK 18(10P15.3) WILD-TYPE 63 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     76   52
  DEL PEAK 18(10P15.3) WILD-TYPE   63   66
        clus
vv       DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  FEMALE                           76                             63
  MALE                             52                             66
[1] 2 2
[1] FALSE
D43V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   83 43
  DEL PEAK 18(10P15.3) WILD-TYPE 96 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     83   43
  DEL PEAK 18(10P15.3) WILD-TYPE   96   29
     clus
vv    DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  NO                            83                             96
  YES                           43                             29
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 18(10P15.3) MUTATED                             17             0
  DEL PEAK 18(10P15.3) WILD-TYPE                           42             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 18(10P15.3) MUTATED                                                                          0
  DEL PEAK 18(10P15.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 18(10P15.3) MUTATED                     63
  DEL PEAK 18(10P15.3) WILD-TYPE                   40
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 18(10P15.3) MUTATED                                                  6
  DEL PEAK 18(10P15.3) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 18(10P15.3) MUTATED                 14
  DEL PEAK 18(10P15.3) WILD-TYPE               10
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 18(10P15.3) MUTATED                                                         12
  DEL PEAK 18(10P15.3) WILD-TYPE                                                       16
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 18(10P15.3) MUTATED                                          0
  DEL PEAK 18(10P15.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 18(10P15.3) MUTATED                             0
  DEL PEAK 18(10P15.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 18(10P15.3) MUTATED                               1
  DEL PEAK 18(10P15.3) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 18(10P15.3) MUTATED                                           15
  DEL PEAK 18(10P15.3) WILD-TYPE                                          6
D43V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 18(10P15.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       17
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               63
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         15
                                                                          clus
vv                                                                         DEL PEAK 18(10P15.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         42
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 40
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                     10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(10P15.3) MUTATED   81 32  2 13
  DEL PEAK 18(10P15.3) WILD-TYPE 71 37  7 13
D43V7, multiclass
    clus
vv   DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  R0                           81                             71
  R1                           32                             37
  R2                            2                              7
  RX                           13                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P15.3) MUTATED       4                        12   107
  DEL PEAK 18(10P15.3) WILD-TYPE     2                         6   117
D43V8, multiclass
                           clus
vv                          DEL PEAK 18(10P15.3) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              107
                           clus
vv                          DEL PEAK 18(10P15.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED     1 112
  DEL PEAK 18(10P15.3) WILD-TYPE   4 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1  112
  DEL PEAK 18(10P15.3) WILD-TYPE    4  108
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 18(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            108
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 19(10Q23.31) MUTATED   80 58
  DEL PEAK 19(10Q23.31) WILD-TYPE 79 40
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            138                             119 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             58                              40 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.18        34.36        75.32        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       12.07        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21        22.62        11.70        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94       188.15        17.52        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        44.91        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1KZ 
       10.32        38.47        36.03        26.56        68.61        45.11 
TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       18.54         6.28        51.02        14.99        10.68        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 
       52.77        46.03        26.47       108.82        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       37.41        82.68        36.33        31.96         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ 
       16.87        86.30        64.21       101.23        62.20         9.34 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       40.77       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T 
        6.58         1.15        17.79        12.00        86.10        77.88 
TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
      106.55        31.13        21.70        20.32        19.89        67.63 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        33.30         0.72        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VE 
        1.38        19.89        25.22       171.09        13.58        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV 
        1.05         3.91       101.26        62.17        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
       63.81        35.28        25.41         0.49        21.73        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       10.45         7.36        37.55        81.01        13.08        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-RN-AAAQ 
       46.82        48.59        35.90        37.12        10.52        16.77 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XQ 
       18.94        22.82         8.61        10.72        12.46         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       84.79        65.46        22.62        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-Z4-AAPG 
       45.34        30.84        35.18        50.86        27.32        15.98 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        34.68        67.20        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-IS-A3K8 TCGA-MB-A5Y9 
       60.00        84.66        32.15        16.60       159.29         8.28 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX 
       26.17        41.49        54.74        42.84        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        32.71        12.85        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       66.94        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE 
       35.77         4.54        73.87        35.28        59.84        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI 
       36.85        26.99        78.28        50.50        21.30        34.49 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BX TCGA-DX-AB2G TCGA-DX-AB2L 
       45.14        47.87        38.17        19.43        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       66.74         9.21        50.40        50.89        71.31        49.15 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IW-A3M4 
       15.48         8.05        34.88         9.80        37.12        85.97 
TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QT TCGA-LI-A67I 
        5.92        53.33       123.78        17.36        16.41        30.31 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       19.73        17.98        22.39        11.57       122.96        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        18.08       130.32       111.98        64.77         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        25.35        32.75        19.63        13.22        13.41 
TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A8C3 TCGA-X6-A8C4 
       11.93        38.27         8.58        63.35        19.17        20.65 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           0.49                            0.56 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         188.15                          159.29 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         26.745                          33.440 
[1] "0.5 - 188.2 (26.7)" "0.6 - 159.3 (33.4)"
[1] "hr=" "1.4"
D44V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 19(10Q23.31) MUTATED                0                  4
  DEL PEAK 19(10Q23.31) WILD-TYPE              1                  3
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 19(10Q23.31) MUTATED                     0                   1
  DEL PEAK 19(10Q23.31) WILD-TYPE                   2                   0
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                               2
  DEL PEAK 19(10Q23.31) WILD-TYPE                             0
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 19(10Q23.31) MUTATED                       1                     17
  DEL PEAK 19(10Q23.31) WILD-TYPE                     0                     11
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 19(10Q23.31) MUTATED                      1                    0
  DEL PEAK 19(10Q23.31) WILD-TYPE                    1                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                                       0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 19(10Q23.31) MUTATED                                  0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                                                2
  DEL PEAK 19(10Q23.31) WILD-TYPE                                              0
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 19(10Q23.31) MUTATED                                 5
  DEL PEAK 19(10Q23.31) WILD-TYPE                               5
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 19(10Q23.31) MUTATED                                         0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 19(10Q23.31) MUTATED                              2
  DEL PEAK 19(10Q23.31) WILD-TYPE                            2
                                 vv
clus                              LOWER EXTREMITY - GROIN
  DEL PEAK 19(10Q23.31) MUTATED                         1
  DEL PEAK 19(10Q23.31) WILD-TYPE                       1
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 19(10Q23.31) MUTATED                                  9
  DEL PEAK 19(10Q23.31) WILD-TYPE                                8
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                                         4
  DEL PEAK 19(10Q23.31) WILD-TYPE                                       1
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 19(10Q23.31) MUTATED                             26
  DEL PEAK 19(10Q23.31) WILD-TYPE                           18
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 19(10Q23.31) MUTATED                                         3
  DEL PEAK 19(10Q23.31) WILD-TYPE                                       1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 19(10Q23.31) MUTATED                                           1
  DEL PEAK 19(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 19(10Q23.31) MUTATED                                                  2
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                3
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 19(10Q23.31) MUTATED                                          5
  DEL PEAK 19(10Q23.31) WILD-TYPE                                        3
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 19(10Q23.31) MUTATED                                                         1
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                       1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 19(10Q23.31) MUTATED                                            1
  DEL PEAK 19(10Q23.31) WILD-TYPE                                          0
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 19(10Q23.31) MUTATED                                                  31
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                42
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 19(10Q23.31) MUTATED                                                    2
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                  1
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 19(10Q23.31) MUTATED                                    2
  DEL PEAK 19(10Q23.31) WILD-TYPE                                  0
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  DEL PEAK 19(10Q23.31) MUTATED                          3
  DEL PEAK 19(10Q23.31) WILD-TYPE                        2
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 19(10Q23.31) MUTATED                             4
  DEL PEAK 19(10Q23.31) WILD-TYPE                           0
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  DEL PEAK 19(10Q23.31) MUTATED                           0
  DEL PEAK 19(10Q23.31) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 19(10Q23.31) MUTATED                                   5
  DEL PEAK 19(10Q23.31) WILD-TYPE                                 2
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 19(10Q23.31) MUTATED                                   3
  DEL PEAK 19(10Q23.31) WILD-TYPE                                 2
D44V3, multiclass
                                                         clus
vv                                                        DEL PEAK 19(10Q23.31) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             17
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        2
  LOWER EXTREMITY - GROIN                                                             1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             4
  LOWER EXTREMITY - THIGH/KNEE                                                       26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  31
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         4
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
                                                         clus
vv                                                        DEL PEAK 19(10Q23.31) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    3
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                                         0
  GYNECOLOGICAL - OVARY                                                                 0
  GYNECOLOGICAL - UTERUS                                                               11
  HEAD AND NECK - HEAD                                                                  1
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          2
  LOWER EXTREMITY - GROIN                                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                                      8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               1
  LOWER EXTREMITY - THIGH/KNEE                                                         18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    42
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    0
  SUPERFICIAL TRUNK - BACK                                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                                           0
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                                 cls
clus                               0  1
  DEL PEAK 19(10Q23.31) MUTATED   80 58
  DEL PEAK 19(10Q23.31) WILD-TYPE 59 60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     80   58
  DEL PEAK 19(10Q23.31) WILD-TYPE   59   60
        clus
vv       DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  FEMALE                            80                              59
  MALE                              58                              60
[1] 2 2
[1] FALSE
D44V5, binary
                                 cls
clus                               0  1
  DEL PEAK 19(10Q23.31) MUTATED   89 45
  DEL PEAK 19(10Q23.31) WILD-TYPE 90 27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     89   45
  DEL PEAK 19(10Q23.31) WILD-TYPE   90   27
     clus
vv    DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  NO                             89                              90
  YES                            45                              27
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 19(10Q23.31) MUTATED                             10             0
  DEL PEAK 19(10Q23.31) WILD-TYPE                           49             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 19(10Q23.31) MUTATED                                                                          0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  DEL PEAK 19(10Q23.31) MUTATED                     79
  DEL PEAK 19(10Q23.31) WILD-TYPE                   24
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 19(10Q23.31) MUTATED                                                  4
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                5
                                 vv
clus                              MYXOFIBROSARCOMA
  DEL PEAK 19(10Q23.31) MUTATED                 14
  DEL PEAK 19(10Q23.31) WILD-TYPE               10
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 19(10Q23.31) MUTATED                                                         16
  DEL PEAK 19(10Q23.31) WILD-TYPE                                                       12
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 19(10Q23.31) MUTATED                                          0
  DEL PEAK 19(10Q23.31) WILD-TYPE                                        2
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 19(10Q23.31) MUTATED                             0
  DEL PEAK 19(10Q23.31) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 19(10Q23.31) MUTATED                               0
  DEL PEAK 19(10Q23.31) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 19(10Q23.31) MUTATED                                           15
  DEL PEAK 19(10Q23.31) WILD-TYPE                                          6
D44V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 19(10Q23.31) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        10
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                79
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     4
  MYXOFIBROSARCOMA                                                                                    14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          15
                                                                          clus
vv                                                                         DEL PEAK 19(10Q23.31) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          49
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  24
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       5
  MYXOFIBROSARCOMA                                                                                      10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                             6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 19(10Q23.31) MUTATED   80 38  6 13
  DEL PEAK 19(10Q23.31) WILD-TYPE 72 31  3 13
D44V7, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  R0                            80                              72
  R1                            38                              31
  R2                             6                               3
  RX                            13                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.31) MUTATED       2                        15   116
  DEL PEAK 19(10Q23.31) WILD-TYPE     4                         3   108
D44V8, multiclass
                           clus
vv                          DEL PEAK 19(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               116
                           clus
vv                          DEL PEAK 19(10Q23.31) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                 108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     1 122
  DEL PEAK 19(10Q23.31) WILD-TYPE   4  98
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      1  122
  DEL PEAK 19(10Q23.31) WILD-TYPE    4   98
                        clus
vv                       DEL PEAK 19(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           122
                        clus
vv                       DEL PEAK 19(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              98
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 20(10Q26.3) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(10Q26.3) MUTATED   80 52
  DEL PEAK 20(10Q26.3) WILD-TYPE 79 46
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           132                            125 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            52                             46 
$`DEL PEAK 20(10Q26.3) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.18        34.36        75.32        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       12.07        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21        22.62        11.70        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94       188.15        17.52        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        68.55        44.91        25.25        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       36.03        18.64        26.56        32.71        68.61        45.11 
TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD 
       33.44        51.02        14.99        10.68        68.55        50.43 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       85.45        45.99        24.26        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ 
       36.33        31.96         3.06        41.00        16.87        86.30 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU 
      101.23        62.20         9.34        40.77        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T 
       60.66         6.58        17.79        12.00        86.10        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
      106.55        50.40        31.13        21.70        20.32        15.48 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EK 
       67.63         4.57        33.30         0.72        80.48         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
       19.89        25.22       171.09        13.58         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV 
        1.05         3.91       101.26        62.17        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
       63.81        35.28        25.41         0.49        21.73        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       10.45         7.36        37.55        81.01        13.08        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z4 
       46.82        48.59        37.12       111.98        16.77        18.94 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XY TCGA-WK-A8Y0 
       22.82         8.61        10.72        12.46        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        8.58        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-Z4-AAPG 
       35.18        19.17        20.65        50.86        27.32        15.98 

$`DEL PEAK 20(10Q26.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        34.68        67.20        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-IS-A3K8 TCGA-MB-A5Y9 
       60.00        84.66        32.15        16.60       159.29         8.28 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX 
       26.17        41.49        88.57        54.74        14.37        42.84 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        0.56        14.04        12.85        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       79.17         9.04        49.05        86.83       136.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J 
       31.86        35.77         4.54        73.87        34.88         9.73 
TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV 
       35.28        28.96        36.85        26.99        78.28        50.50 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21        21.30        34.49        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        20.05        61.97        45.14        47.87        38.17 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2L 
      150.35        40.44        19.43         1.15        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A48G 
       66.74         9.21        50.89        71.31        49.15        19.89 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A3RQ 
        8.05        34.88         9.80        19.53         3.22        37.12 
TCGA-IW-A3M4 TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QT TCGA-LI-A67I 
       85.97        53.33       123.78        17.36        16.41        30.31 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       19.73        17.98        22.39        11.57       122.96        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
        1.84        18.08        35.90       130.32        64.77        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
        0.72         3.88        25.35        32.75        19.63        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T 
       13.41        11.93         4.80        84.79        38.27        63.35 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                          0.49                           0.56 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                        27.125                         33.530 
[1] "0.5 - 188.2 (27.1)" "0.6 - 159.3 (33.5)"
[1] "hr=" "1.2"
D45V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 20(10Q26.3) MUTATED                0                  4
  DEL PEAK 20(10Q26.3) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 20(10Q26.3) MUTATED                     0                   1
  DEL PEAK 20(10Q26.3) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 20(10Q26.3) MUTATED                               1
  DEL PEAK 20(10Q26.3) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 20(10Q26.3) MUTATED                       1                     19
  DEL PEAK 20(10Q26.3) WILD-TYPE                     0                      9
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 20(10Q26.3) MUTATED                      1                    0
  DEL PEAK 20(10Q26.3) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 20(10Q26.3) MUTATED                                       0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 20(10Q26.3) MUTATED                                  0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 20(10Q26.3) MUTATED                                                2
  DEL PEAK 20(10Q26.3) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 20(10Q26.3) MUTATED                                 5
  DEL PEAK 20(10Q26.3) WILD-TYPE                               5
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 20(10Q26.3) MUTATED                                         0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 20(10Q26.3) MUTATED                              2
  DEL PEAK 20(10Q26.3) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 20(10Q26.3) MUTATED                         1
  DEL PEAK 20(10Q26.3) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 20(10Q26.3) MUTATED                                 12
  DEL PEAK 20(10Q26.3) WILD-TYPE                                5
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 20(10Q26.3) MUTATED                                         4
  DEL PEAK 20(10Q26.3) WILD-TYPE                                       1
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 20(10Q26.3) MUTATED                             21
  DEL PEAK 20(10Q26.3) WILD-TYPE                           23
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 20(10Q26.3) MUTATED                                         3
  DEL PEAK 20(10Q26.3) WILD-TYPE                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 20(10Q26.3) MUTATED                                           0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 20(10Q26.3) MUTATED                                                  1
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 20(10Q26.3) MUTATED                                          5
  DEL PEAK 20(10Q26.3) WILD-TYPE                                        3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 20(10Q26.3) MUTATED                                                         1
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 20(10Q26.3) MUTATED                                            1
  DEL PEAK 20(10Q26.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 20(10Q26.3) MUTATED                                                  30
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                43
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 20(10Q26.3) MUTATED                                                    2
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 20(10Q26.3) MUTATED                                    2
  DEL PEAK 20(10Q26.3) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 20(10Q26.3) MUTATED                          2
  DEL PEAK 20(10Q26.3) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 20(10Q26.3) MUTATED                             4
  DEL PEAK 20(10Q26.3) WILD-TYPE                           0
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 20(10Q26.3) MUTATED                           0
  DEL PEAK 20(10Q26.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 20(10Q26.3) MUTATED                                   4
  DEL PEAK 20(10Q26.3) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 20(10Q26.3) MUTATED                                   3
  DEL PEAK 20(10Q26.3) WILD-TYPE                                 2
D45V3, multiclass
                                                         clus
vv                                                        DEL PEAK 20(10Q26.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            19
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            4
  LOWER EXTREMITY - THIGH/KNEE                                                      21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 30
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        DEL PEAK 20(10Q26.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                               9
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              1
  LOWER EXTREMITY - THIGH/KNEE                                                        23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   43
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          0
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED   75 57
  DEL PEAK 20(10Q26.3) WILD-TYPE 64 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     75   57
  DEL PEAK 20(10Q26.3) WILD-TYPE   64   61
        clus
vv       DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  FEMALE                           75                             64
  MALE                             57                             61
[1] 2 2
[1] FALSE
D45V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED   88 41
  DEL PEAK 20(10Q26.3) WILD-TYPE 91 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     88   41
  DEL PEAK 20(10Q26.3) WILD-TYPE   91   31
     clus
vv    DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  NO                            88                             91
  YES                           41                             31
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 20(10Q26.3) MUTATED                              9             0
  DEL PEAK 20(10Q26.3) WILD-TYPE                           50             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 20(10Q26.3) MUTATED                                                                          0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 20(10Q26.3) MUTATED                     77
  DEL PEAK 20(10Q26.3) WILD-TYPE                   26
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 20(10Q26.3) MUTATED                                                  3
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 20(10Q26.3) MUTATED                 14
  DEL PEAK 20(10Q26.3) WILD-TYPE               10
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 20(10Q26.3) MUTATED                                                         14
  DEL PEAK 20(10Q26.3) WILD-TYPE                                                       14
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 20(10Q26.3) MUTATED                                          0
  DEL PEAK 20(10Q26.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 20(10Q26.3) MUTATED                             0
  DEL PEAK 20(10Q26.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 20(10Q26.3) MUTATED                               0
  DEL PEAK 20(10Q26.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 20(10Q26.3) MUTATED                                           15
  DEL PEAK 20(10Q26.3) WILD-TYPE                                          6
D45V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 20(10Q26.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        9
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               77
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         15
                                                                          clus
vv                                                                         DEL PEAK 20(10Q26.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         50
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 26
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(10Q26.3) MUTATED   78 35  5 13
  DEL PEAK 20(10Q26.3) WILD-TYPE 74 34  4 13
D45V7, multiclass
    clus
vv   DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  R0                           78                             74
  R1                           35                             34
  R2                            5                              4
  RX                           13                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q26.3) MUTATED       3                        14   110
  DEL PEAK 20(10Q26.3) WILD-TYPE     3                         4   114
D45V8, multiclass
                           clus
vv                          DEL PEAK 20(10Q26.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              110
                           clus
vv                          DEL PEAK 20(10Q26.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                                cls
clus                               0   1
  DEL PEAK 20(10Q26.3) MUTATED     1 117
  DEL PEAK 20(10Q26.3) WILD-TYPE   4 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      1  117
  DEL PEAK 20(10Q26.3) WILD-TYPE    4  103
                        clus
vv                       DEL PEAK 20(10Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       DEL PEAK 20(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            103
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11P15.5) MUTATED   63 47
  DEL PEAK 21(11P15.5) WILD-TYPE 96 51
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           110                            147 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            47                             51 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB35 
       31.53        67.20        34.36        17.95        14.43        30.51 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK 
       60.00        32.15        37.02        12.62        52.11        52.27 
TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-VT-A80J TCGA-X6-A8C6 
       22.62        17.75         6.35       188.15        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I0 
       50.01        19.69        44.91        14.37        42.84        36.03 
TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 
       18.64        14.04        32.71        68.61        45.11        85.02 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY 
        6.28         9.70         9.04        49.05       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE 
       44.68        31.86        51.02        14.99        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6B8 
       85.45        24.26        35.28        52.77        46.03        15.95 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
        3.06        78.28        86.30        34.49        62.20        30.35 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BV 
       61.97        45.14        47.87        40.77        36.69        60.66 
TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-FX-A3RE 
       12.00        66.74        77.88       106.55        50.89        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       20.32        19.89        67.63         4.57        33.30         0.72 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN 
       19.53        19.89        25.22         5.92         1.05       101.26 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 
       62.17        23.38         5.19        63.81        16.41        25.41 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       37.55        81.01        35.90        10.52        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU 
       22.82        25.35        32.75         8.61        19.63        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       10.72        12.46        38.27        65.46        22.62         8.58 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C5 
       26.43        35.90        18.08        45.34        20.65        50.86 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BP 
       36.30        34.68        16.18        75.32        15.22        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       15.85        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
      101.98        84.66        16.60        26.93        28.21       159.29 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-WK-A8XT 
       11.70         8.28        18.08        20.94        17.52        41.49 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       53.49        68.55        88.57        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       38.47        26.56         0.56        12.85        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU 
       27.81        60.30         8.58        95.38        79.17        86.83 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J 
       35.77         4.54        10.68        73.87        68.55         9.73 
TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       45.99        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        50.50        16.87        64.21       101.23        21.30 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BN 
      152.12        29.49        48.20        20.05         9.34        38.17 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
      150.35        27.95        40.44        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2Z 
       17.79        15.72        65.98        86.10         9.21        50.40 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       71.31        49.15        31.13        15.48         8.05        34.88 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 
        9.80        80.48         3.22         1.38        37.12       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
       13.58        85.97        16.41         3.91        53.33       123.78 
TCGA-K1-A6RT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       17.36        35.28        30.31         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
      122.96        38.63        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        37.12       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        0.72        16.77        13.22        11.93         4.80        84.79 
TCGA-X2-A95T TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A973 
       63.35        30.84        35.18        19.17        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        188.15                         171.09 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                         32.43                          29.49 
[1] "0.7 - 188.2 (32.4)" "0.5 - 171.1 (29.5)"
[1] "hr=" "1.3"
D46V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 21(11P15.5) MUTATED                0                  4
  DEL PEAK 21(11P15.5) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 21(11P15.5) MUTATED                     0                   0
  DEL PEAK 21(11P15.5) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 21(11P15.5) MUTATED                               2
  DEL PEAK 21(11P15.5) WILD-TYPE                             0
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 21(11P15.5) MUTATED                       1                     13
  DEL PEAK 21(11P15.5) WILD-TYPE                     0                     15
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 21(11P15.5) MUTATED                      0                    0
  DEL PEAK 21(11P15.5) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 21(11P15.5) MUTATED                                       0
  DEL PEAK 21(11P15.5) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 21(11P15.5) MUTATED                                  0
  DEL PEAK 21(11P15.5) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 21(11P15.5) MUTATED                                                1
  DEL PEAK 21(11P15.5) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 21(11P15.5) MUTATED                                 2
  DEL PEAK 21(11P15.5) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 21(11P15.5) MUTATED                                         0
  DEL PEAK 21(11P15.5) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 21(11P15.5) MUTATED                              1
  DEL PEAK 21(11P15.5) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 21(11P15.5) MUTATED                         0
  DEL PEAK 21(11P15.5) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 21(11P15.5) MUTATED                                  8
  DEL PEAK 21(11P15.5) WILD-TYPE                                9
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 21(11P15.5) MUTATED                                         5
  DEL PEAK 21(11P15.5) WILD-TYPE                                       0
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 21(11P15.5) MUTATED                             20
  DEL PEAK 21(11P15.5) WILD-TYPE                           24
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 21(11P15.5) MUTATED                                         1
  DEL PEAK 21(11P15.5) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 21(11P15.5) MUTATED                                           0
  DEL PEAK 21(11P15.5) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 21(11P15.5) MUTATED                                                  1
  DEL PEAK 21(11P15.5) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 21(11P15.5) MUTATED                                          4
  DEL PEAK 21(11P15.5) WILD-TYPE                                        4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 21(11P15.5) MUTATED                                                         0
  DEL PEAK 21(11P15.5) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 21(11P15.5) MUTATED                                            1
  DEL PEAK 21(11P15.5) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 21(11P15.5) MUTATED                                                  31
  DEL PEAK 21(11P15.5) WILD-TYPE                                                42
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 21(11P15.5) MUTATED                                                    2
  DEL PEAK 21(11P15.5) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 21(11P15.5) MUTATED                                    1
  DEL PEAK 21(11P15.5) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 21(11P15.5) MUTATED                          2
  DEL PEAK 21(11P15.5) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 21(11P15.5) MUTATED                             2
  DEL PEAK 21(11P15.5) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 21(11P15.5) MUTATED                           0
  DEL PEAK 21(11P15.5) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 21(11P15.5) MUTATED                                   4
  DEL PEAK 21(11P15.5) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 21(11P15.5) MUTATED                                   3
  DEL PEAK 21(11P15.5) WILD-TYPE                                 2
D46V3, multiclass
                                                         clus
vv                                                        DEL PEAK 21(11P15.5) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            13
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            5
  LOWER EXTREMITY - THIGH/KNEE                                                      20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 31
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        DEL PEAK 21(11P15.5) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        0
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              15
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              0
  LOWER EXTREMITY - THIGH/KNEE                                                        24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   42
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED   62 48
  DEL PEAK 21(11P15.5) WILD-TYPE 77 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     62   48
  DEL PEAK 21(11P15.5) WILD-TYPE   77   70
        clus
vv       DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  FEMALE                           62                             77
  MALE                             48                             70
[1] 2 2
[1] FALSE
D46V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED    71  38
  DEL PEAK 21(11P15.5) WILD-TYPE 108  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     71   38
  DEL PEAK 21(11P15.5) WILD-TYPE  108   34
     clus
vv    DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  NO                            71                            108
  YES                           38                             34
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 21(11P15.5) MUTATED                             23             0
  DEL PEAK 21(11P15.5) WILD-TYPE                           36             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 21(11P15.5) MUTATED                                                                          0
  DEL PEAK 21(11P15.5) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 21(11P15.5) MUTATED                     46
  DEL PEAK 21(11P15.5) WILD-TYPE                   57
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 21(11P15.5) MUTATED                                                  6
  DEL PEAK 21(11P15.5) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 21(11P15.5) MUTATED                 12
  DEL PEAK 21(11P15.5) WILD-TYPE               12
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 21(11P15.5) MUTATED                                                          9
  DEL PEAK 21(11P15.5) WILD-TYPE                                                       19
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 21(11P15.5) MUTATED                                          0
  DEL PEAK 21(11P15.5) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 21(11P15.5) MUTATED                             0
  DEL PEAK 21(11P15.5) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 21(11P15.5) MUTATED                               1
  DEL PEAK 21(11P15.5) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 21(11P15.5) MUTATED                                           13
  DEL PEAK 21(11P15.5) WILD-TYPE                                          8
D46V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 21(11P15.5) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       23
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               46
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         13
                                                                          clus
vv                                                                         DEL PEAK 21(11P15.5) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         36
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 57
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                     12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 21(11P15.5) MUTATED   61 32  5 12
  DEL PEAK 21(11P15.5) WILD-TYPE 91 37  4 14
D46V7, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  R0                           61                             91
  R1                           32                             37
  R2                            5                              4
  RX                           12                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED       2                         6    97
  DEL PEAK 21(11P15.5) WILD-TYPE     4                        12   127
D46V8, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               97
                           clus
vv                          DEL PEAK 21(11P15.5) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  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"
D46V9, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED     1  99
  DEL PEAK 21(11P15.5) WILD-TYPE   4 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      1   99
  DEL PEAK 21(11P15.5) WILD-TYPE    4  121
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            121
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 22(11Q23.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(11Q23.1) MUTATED   75 43
  DEL PEAK 22(11Q23.1) WILD-TYPE 84 55
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                           118                            139 
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                            43                             55 
$`DEL PEAK 22(11Q23.1) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       31.53        34.68        16.18        34.36        15.22        17.95 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-FX-A3NK 
       12.07       106.45       101.98        30.51        84.66        16.60 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 
       12.62        52.11        52.27        22.62        11.70         8.28 
TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HR TCGA-3B-A9HS 
        6.35       188.15        35.08        50.01        88.57        44.91 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX 
       25.25        14.37        42.84        38.47        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23R 
       14.04        32.71        68.61        45.11        18.54        74.66 
TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LY TCGA-DX-A3M1 
        5.26         6.28         9.70        95.38        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       31.86        51.02        50.43        45.99        35.28        52.77 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       26.47       108.82        82.68        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK 
       78.28        86.30        64.21        34.49        62.20        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O 
       40.44        36.69        60.66        12.00        15.72        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-FX-A2QS TCGA-HB-A2OT 
       66.74        77.88       106.55        50.89        49.15        67.63 
TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M5 
        4.57        80.48        19.89        37.12        13.58         5.92 
TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
        1.05        62.17       123.78        23.38         5.19        63.81 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MO-A47R TCGA-N1-A6IA 
       35.28        30.31        25.41        21.73        10.45         7.36 
TCGA-QC-AA9N TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
       17.65        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
       32.75         8.61        19.63        10.72        12.46        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
       38.27        65.46        22.62         8.58        26.43        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
       35.18        19.17        20.65        27.32 

$`DEL PEAK 22(11Q23.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        67.20        75.32        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-HB-A43Z 
       40.60        13.28        22.85        60.00        32.15        37.02 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-PC-A5DP TCGA-QC-A6FX 
       26.93        28.21       159.29        17.75        18.08        20.94 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        19.69        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KY TCGA-DX-A1L1 
       54.74        10.32        36.03        18.64        12.85        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       85.02        33.53        66.94        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
       60.30         8.58        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
      136.44        35.77         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P 
       68.55        34.88        85.45         9.73        24.26        46.03 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF 
       36.85        26.99        50.50        16.87       101.23        21.30 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2L TCGA-DX-AB2S 
       19.43         6.58         1.15        17.79        65.98         9.21 
TCGA-DX-AB2Z TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       50.40        71.31        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       15.48         8.05        34.88        33.30         0.72         9.80 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 
       19.53         3.22         1.38        25.22       171.09        85.97 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-KD-A5QT 
       16.41         3.91       101.26        53.33        17.36        16.41 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        22.39        11.57 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 
      122.96        37.55        38.63        81.01        13.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-UE-A6QU 
      111.98        64.77        10.52         0.72        13.22        13.41 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       11.93         4.80        63.35        35.90        18.08        30.84 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       50.86        29.46        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                          0.56                           0.49 
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                        188.15                         171.09 
  DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE 
                         33.90                          28.21 
[1] "0.6 - 188.2 (33.9)" "0.5 - 171.1 (28.2)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 22(11Q23.1) MUTATED                0                  5
  DEL PEAK 22(11Q23.1) WILD-TYPE              1                  2
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 22(11Q23.1) MUTATED                     0                   1
  DEL PEAK 22(11Q23.1) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 22(11Q23.1) MUTATED                               0
  DEL PEAK 22(11Q23.1) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 22(11Q23.1) MUTATED                       0                     11
  DEL PEAK 22(11Q23.1) WILD-TYPE                     1                     17
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 22(11Q23.1) MUTATED                      0                    0
  DEL PEAK 22(11Q23.1) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 22(11Q23.1) MUTATED                                       0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 22(11Q23.1) MUTATED                                  0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 22(11Q23.1) MUTATED                                                0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 22(11Q23.1) MUTATED                                 3
  DEL PEAK 22(11Q23.1) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 22(11Q23.1) MUTATED                                         0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 22(11Q23.1) MUTATED                              1
  DEL PEAK 22(11Q23.1) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 22(11Q23.1) MUTATED                         0
  DEL PEAK 22(11Q23.1) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 22(11Q23.1) MUTATED                                  9
  DEL PEAK 22(11Q23.1) WILD-TYPE                                8
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 22(11Q23.1) MUTATED                                         5
  DEL PEAK 22(11Q23.1) WILD-TYPE                                       0
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 22(11Q23.1) MUTATED                             28
  DEL PEAK 22(11Q23.1) WILD-TYPE                           16
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 22(11Q23.1) MUTATED                                         1
  DEL PEAK 22(11Q23.1) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 22(11Q23.1) MUTATED                                           2
  DEL PEAK 22(11Q23.1) WILD-TYPE                                         0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 22(11Q23.1) MUTATED                                                  2
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 22(11Q23.1) MUTATED                                          4
  DEL PEAK 22(11Q23.1) WILD-TYPE                                        4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 22(11Q23.1) MUTATED                                                         1
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 22(11Q23.1) MUTATED                                            1
  DEL PEAK 22(11Q23.1) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 22(11Q23.1) MUTATED                                                  31
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                42
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 22(11Q23.1) MUTATED                                                    1
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                  2
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 22(11Q23.1) MUTATED                                    1
  DEL PEAK 22(11Q23.1) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 22(11Q23.1) MUTATED                          1
  DEL PEAK 22(11Q23.1) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 22(11Q23.1) MUTATED                             3
  DEL PEAK 22(11Q23.1) WILD-TYPE                           1
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 22(11Q23.1) MUTATED                           0
  DEL PEAK 22(11Q23.1) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 22(11Q23.1) MUTATED                                   4
  DEL PEAK 22(11Q23.1) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 22(11Q23.1) MUTATED                                   2
  DEL PEAK 22(11Q23.1) WILD-TYPE                                 3
D47V3, multiclass
                                                         clus
vv                                                        DEL PEAK 22(11Q23.1) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 5
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                            11
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            5
  LOWER EXTREMITY - THIGH/KNEE                                                      28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 31
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK 22(11Q23.1) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   2
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              17
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              0
  LOWER EXTREMITY - THIGH/KNEE                                                        16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   42
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          1
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                                cls
clus                              0  1
  DEL PEAK 22(11Q23.1) MUTATED   63 55
  DEL PEAK 22(11Q23.1) WILD-TYPE 76 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.1) MUTATED     63   55
  DEL PEAK 22(11Q23.1) WILD-TYPE   76   63
        clus
vv       DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE
  FEMALE                           63                             76
  MALE                             55                             63
[1] 2 2
[1] FALSE
D47V5, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.1) MUTATED    73  45
  DEL PEAK 22(11Q23.1) WILD-TYPE 106  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.1) MUTATED     73   45
  DEL PEAK 22(11Q23.1) WILD-TYPE  106   27
     clus
vv    DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE
  NO                            73                            106
  YES                           45                             27
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 22(11Q23.1) MUTATED                             29             0
  DEL PEAK 22(11Q23.1) WILD-TYPE                           30             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 22(11Q23.1) MUTATED                                                                          0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 22(11Q23.1) MUTATED                     38
  DEL PEAK 22(11Q23.1) WILD-TYPE                   65
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 22(11Q23.1) MUTATED                                                  6
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 22(11Q23.1) MUTATED                 16
  DEL PEAK 22(11Q23.1) WILD-TYPE                8
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 22(11Q23.1) MUTATED                                                         16
  DEL PEAK 22(11Q23.1) WILD-TYPE                                                       12
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 22(11Q23.1) MUTATED                                          0
  DEL PEAK 22(11Q23.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 22(11Q23.1) MUTATED                             0
  DEL PEAK 22(11Q23.1) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 22(11Q23.1) MUTATED                               1
  DEL PEAK 22(11Q23.1) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 22(11Q23.1) MUTATED                                           12
  DEL PEAK 22(11Q23.1) WILD-TYPE                                          9
D47V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 22(11Q23.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       29
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               38
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         12
                                                                          clus
vv                                                                         DEL PEAK 22(11Q23.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         30
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 65
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                      8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(11Q23.1) MUTATED   63 38  4 12
  DEL PEAK 22(11Q23.1) WILD-TYPE 89 31  5 14
D47V7, multiclass
    clus
vv   DEL PEAK 22(11Q23.1) MUTATED DEL PEAK 22(11Q23.1) WILD-TYPE
  R0                           63                             89
  R1                           38                             31
  R2                            4                              5
  RX                           12                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q23.1) MUTATED       3                        10   102
  DEL PEAK 22(11Q23.1) WILD-TYPE     3                         8   122
D47V8, multiclass
                           clus
vv                          DEL PEAK 22(11Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              102
                           clus
vv                          DEL PEAK 22(11Q23.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.1) MUTATED     1 104
  DEL PEAK 22(11Q23.1) WILD-TYPE   4 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.1) MUTATED      1  104
  DEL PEAK 22(11Q23.1) WILD-TYPE    4  116
                        clus
vv                       DEL PEAK 22(11Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 22(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            116
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 23(11Q25) MUTATION ANALYSIS
D48V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 23(11Q25) MUTATED   73 50
  DEL PEAK 23(11Q25) WILD-TYPE 86 48
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         123                          134 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                          50                           48 
$`DEL PEAK 23(11Q25) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       31.53        34.68        16.18        34.36        15.22        17.95 
TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 
       14.07        12.07       106.45       101.98        30.51        84.66 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       12.62        52.11        52.27        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI 
        8.28         6.35       188.15        26.17        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       19.69        88.57        44.91        25.25        14.37        42.84 
TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       38.47        26.56         0.56        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y 
       45.11        18.54        54.21        74.66         5.26         6.28 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 
        9.70        95.38        49.05        44.68        31.86        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       14.99        50.43        45.99        24.26        35.28        52.77 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       26.47       108.82        82.68        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK 
       78.28        86.30        64.21        34.49        62.20        61.97 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       47.87        38.17        40.77        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V 
       60.66        12.00        15.72        86.10        66.74       106.55 
TCGA-DX-AB3B TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV 
       50.89        20.32        67.63         4.57         0.72        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22        19.89        37.12        13.58         5.92         1.05 
TCGA-K1-A42W TCGA-KD-A5QS TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK 
       62.17        63.81        35.28        30.31        25.41        21.73 
TCGA-MO-A47R TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       10.45        17.65        46.82        18.08        48.59        35.90 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
        8.61        19.63        13.41        10.72        12.46        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
       38.27        65.46        22.62         8.58        26.43        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.18        19.17        20.65 

$`DEL PEAK 23(11Q25) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       36.30        67.20        75.32        14.43        15.85        40.60 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       13.28        22.85        60.00        32.15        16.60        37.02 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       26.93        28.21       159.29        18.08        20.94        17.52 
TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I0 
       41.49        53.49        68.55        54.74        10.32        36.03 
TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U 
       18.64        14.04        85.02        33.53        66.94        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS 
       66.87        27.81        60.30         8.58        79.17         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA 
       86.83       136.44        33.44        35.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48P 
       73.87        68.55        34.88        85.45         9.73        46.03 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF 
       36.85        26.99        50.50        16.87       101.23        21.30 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       45.14       150.35        19.43         6.58         1.15        17.79 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3C TCGA-FX-A2QS 
       65.98         9.21        77.88        50.40        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       31.13        21.70        19.89        15.48         8.05        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 
       33.30         9.80        19.53         1.38        25.22       171.09 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       85.97        16.41         3.91       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MB-A8JL 
       17.36        23.38         5.19        16.41         0.49        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        22.39        11.57         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VD 
       37.55        38.63        81.01        13.08         1.84        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT 
      130.32       111.98        64.77        10.52         0.72        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       11.93         4.80        63.35        35.90        18.08        30.84 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                        0.56                         0.49 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                      188.15                       171.09 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                       31.96                        29.92 
[1] "0.6 - 188.2 (32.0)" "0.5 - 171.1 (29.9)"
[1] "hr=" "1.2"
D48V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 23(11Q25) MUTATED                0                  5
  DEL PEAK 23(11Q25) WILD-TYPE              1                  2
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 23(11Q25) MUTATED                     0                   1
  DEL PEAK 23(11Q25) WILD-TYPE                   2                   0
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 23(11Q25) MUTATED                               0
  DEL PEAK 23(11Q25) WILD-TYPE                             2
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 23(11Q25) MUTATED                       0                     10
  DEL PEAK 23(11Q25) WILD-TYPE                     1                     18
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 23(11Q25) MUTATED                      0                    0
  DEL PEAK 23(11Q25) WILD-TYPE                    2                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 23(11Q25) MUTATED                                       0
  DEL PEAK 23(11Q25) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 23(11Q25) MUTATED                                  0
  DEL PEAK 23(11Q25) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 23(11Q25) MUTATED                                                1
  DEL PEAK 23(11Q25) WILD-TYPE                                              1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 23(11Q25) MUTATED                                 3
  DEL PEAK 23(11Q25) WILD-TYPE                               7
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 23(11Q25) MUTATED                                         0
  DEL PEAK 23(11Q25) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 23(11Q25) MUTATED                              1
  DEL PEAK 23(11Q25) WILD-TYPE                            3
                              vv
clus                           LOWER EXTREMITY - GROIN
  DEL PEAK 23(11Q25) MUTATED                         1
  DEL PEAK 23(11Q25) WILD-TYPE                       1
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 23(11Q25) MUTATED                                 12
  DEL PEAK 23(11Q25) WILD-TYPE                                5
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 23(11Q25) MUTATED                                         5
  DEL PEAK 23(11Q25) WILD-TYPE                                       0
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 23(11Q25) MUTATED                             27
  DEL PEAK 23(11Q25) WILD-TYPE                           17
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 23(11Q25) MUTATED                                         1
  DEL PEAK 23(11Q25) WILD-TYPE                                       3
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 23(11Q25) MUTATED                                           1
  DEL PEAK 23(11Q25) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 23(11Q25) MUTATED                                                  2
  DEL PEAK 23(11Q25) WILD-TYPE                                                3
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 23(11Q25) MUTATED                                          4
  DEL PEAK 23(11Q25) WILD-TYPE                                        4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 23(11Q25) MUTATED                                                         0
  DEL PEAK 23(11Q25) WILD-TYPE                                                       2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 23(11Q25) MUTATED                                            1
  DEL PEAK 23(11Q25) WILD-TYPE                                          0
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 23(11Q25) MUTATED                                                  35
  DEL PEAK 23(11Q25) WILD-TYPE                                                38
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 23(11Q25) MUTATED                                                    1
  DEL PEAK 23(11Q25) WILD-TYPE                                                  2
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 23(11Q25) MUTATED                                    1
  DEL PEAK 23(11Q25) WILD-TYPE                                  1
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  DEL PEAK 23(11Q25) MUTATED                          1
  DEL PEAK 23(11Q25) WILD-TYPE                        4
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 23(11Q25) MUTATED                             3
  DEL PEAK 23(11Q25) WILD-TYPE                           1
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  DEL PEAK 23(11Q25) MUTATED                           0
  DEL PEAK 23(11Q25) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 23(11Q25) MUTATED                                   3
  DEL PEAK 23(11Q25) WILD-TYPE                                 4
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 23(11Q25) MUTATED                                   3
  DEL PEAK 23(11Q25) WILD-TYPE                                 2
D48V3, multiclass
                                                         clus
vv                                                        DEL PEAK 23(11Q25) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               5
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              1
  CHEST - OTHER (PLEASE SPECIFY                                                    0
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                          10
  HEAD AND NECK - HEAD                                                             0
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     1
  LOWER EXTREMITY - GROIN                                                          1
  LOWER EXTREMITY - LOWER LEG/CALF                                                12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          5
  LOWER EXTREMITY - THIGH/KNEE                                                    27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               35
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               1
  SUPERFICIAL TRUNK - BACK                                                         1
  SUPERFICIAL TRUNK - BUTTOCK                                                      3
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                3
                                                         clus
vv                                                        DEL PEAK 23(11Q25) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            18
  HEAD AND NECK - HEAD                                                               2
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       3
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            0
  LOWER EXTREMITY - THIGH/KNEE                                                      17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 38
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           4
  SUPERFICIAL TRUNK - BUTTOCK                                                        1
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                              cls
clus                            0  1
  DEL PEAK 23(11Q25) MUTATED   65 58
  DEL PEAK 23(11Q25) WILD-TYPE 74 60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     65   58
  DEL PEAK 23(11Q25) WILD-TYPE   74   60
        clus
vv       DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  FEMALE                         65                           74
  MALE                           58                           60
[1] 2 2
[1] FALSE
D48V5, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    77  45
  DEL PEAK 23(11Q25) WILD-TYPE 102  27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     77   45
  DEL PEAK 23(11Q25) WILD-TYPE  102   27
     clus
vv    DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  NO                          77                          102
  YES                         45                           27
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 23(11Q25) MUTATED                             30             0
  DEL PEAK 23(11Q25) WILD-TYPE                           29             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 23(11Q25) MUTATED                                                                          0
  DEL PEAK 23(11Q25) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  DEL PEAK 23(11Q25) MUTATED                     39
  DEL PEAK 23(11Q25) WILD-TYPE                   64
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 23(11Q25) MUTATED                                                  6
  DEL PEAK 23(11Q25) WILD-TYPE                                                3
                              vv
clus                           MYXOFIBROSARCOMA
  DEL PEAK 23(11Q25) MUTATED                 14
  DEL PEAK 23(11Q25) WILD-TYPE               10
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 23(11Q25) MUTATED                                                         16
  DEL PEAK 23(11Q25) WILD-TYPE                                                       12
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 23(11Q25) MUTATED                                          0
  DEL PEAK 23(11Q25) WILD-TYPE                                        2
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 23(11Q25) MUTATED                             0
  DEL PEAK 23(11Q25) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 23(11Q25) MUTATED                               1
  DEL PEAK 23(11Q25) WILD-TYPE                             5
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 23(11Q25) MUTATED                                           17
  DEL PEAK 23(11Q25) WILD-TYPE                                          4
D48V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 23(11Q25) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     30
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             39
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  6
  MYXOFIBROSARCOMA                                                                                 14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          0
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                       17
                                                                          clus
vv                                                                         DEL PEAK 23(11Q25) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       29
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               64
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            2
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 23(11Q25) MUTATED   62 43  5 12
  DEL PEAK 23(11Q25) WILD-TYPE 90 26  4 14
D48V7, multiclass
    clus
vv   DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  R0                         62                           90
  R1                         43                           26
  R2                          5                            4
  RX                         12                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q25) MUTATED       4                         8   107
  DEL PEAK 23(11Q25) WILD-TYPE     2                        10   117
D48V8, multiclass
                           clus
vv                          DEL PEAK 23(11Q25) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          8
  WHITE                                            107
                           clus
vv                          DEL PEAK 23(11Q25) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED     1 108
  DEL PEAK 23(11Q25) WILD-TYPE   4 112
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED      1  108
  DEL PEAK 23(11Q25) WILD-TYPE    4  112
                        clus
vv                       DEL PEAK 23(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                        108
                        clus
vv                       DEL PEAK 23(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          112
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 24(12P13.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(12P13.1) MUTATED    52  35
  DEL PEAK 24(12P13.1) WILD-TYPE 107  63
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            87                            170 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            35                             63 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB2H 
       34.68        16.18        67.20        34.36        15.22        15.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-KF-A41W 
      101.98        30.51        16.60        52.11        28.21        11.70 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QC-A6FX TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HV 
       17.75         6.35        20.94        35.08        50.01        14.37 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       18.64        26.56         0.56        32.71        68.61        18.54 
TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW 
       54.21        74.66         6.28         9.70        49.05       136.44 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48N 
       33.44        31.86        51.02        14.99        50.43        35.28 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YZ 
       59.84        37.58        15.95         3.06        41.00        86.30 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL 
      101.23        21.30        62.20        30.35        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU 
       47.87        38.17        40.77       150.35        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2T TCGA-DX-AB2Z 
       60.66        19.43         6.58         1.15        77.88        50.40 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-IE-A6BZ TCGA-JV-A5VF 
       31.13        20.32        34.88        33.30        19.89         1.05 
TCGA-K1-A6RV TCGA-KD-A5QU TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V9 
        5.19        35.28        14.99        81.01        13.08        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 
       48.59        35.90        37.12       111.98        10.52        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX 
        3.88        22.82        13.41        12.46        84.79        38.27 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD 
       63.35        26.43        30.84 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        31.53        75.32        17.95        14.43        14.07 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
       40.60        12.07       106.45        13.28        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK 
       84.66        32.15        37.02        12.62        26.93        52.27 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 
      159.29        22.62         8.28        18.08       188.15        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       26.17        41.49        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        54.74        25.25        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       36.03        14.04        12.85        45.11        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 
        8.58        95.38        79.17         9.04        86.83        44.68 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       35.77         4.54        10.68        73.87        68.55        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       85.45         9.73        45.99        24.26        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47       108.82        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       31.96        36.85        26.99        78.28        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       64.21        34.49       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BT TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
        9.34        40.44        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C 
       86.10        66.74         9.21       106.55        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       49.15        21.70        19.89        15.48         8.05        67.63 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57         0.72         9.80        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        37.12        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
      123.78        17.36        23.38        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       25.41         0.49        21.73        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       17.65         1.84        18.08       130.32        64.77         0.72 
TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       16.77        25.35        32.75         8.61        19.63        13.22 
TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       10.72        11.93         4.80        65.46        22.62         8.58 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        45.34        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          0.56                           0.49 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        150.35                         188.15 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                         33.30                          29.21 
[1] "0.6 - 150.3 (33.3)" "0.5 - 188.2 (29.2)"
[1] "hr=" "1.1"
D49V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 24(12P13.1) MUTATED                0                  3
  DEL PEAK 24(12P13.1) WILD-TYPE              1                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 24(12P13.1) MUTATED                     0                   0
  DEL PEAK 24(12P13.1) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 24(12P13.1) MUTATED                               1
  DEL PEAK 24(12P13.1) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 24(12P13.1) MUTATED                       0                      8
  DEL PEAK 24(12P13.1) WILD-TYPE                     1                     20
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 24(12P13.1) MUTATED                      1                    0
  DEL PEAK 24(12P13.1) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 24(12P13.1) MUTATED                                       0
  DEL PEAK 24(12P13.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 24(12P13.1) MUTATED                                  0
  DEL PEAK 24(12P13.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 24(12P13.1) MUTATED                                                2
  DEL PEAK 24(12P13.1) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 24(12P13.1) MUTATED                                 2
  DEL PEAK 24(12P13.1) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 24(12P13.1) MUTATED                                         0
  DEL PEAK 24(12P13.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 24(12P13.1) MUTATED                              1
  DEL PEAK 24(12P13.1) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 24(12P13.1) MUTATED                         1
  DEL PEAK 24(12P13.1) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 24(12P13.1) MUTATED                                  4
  DEL PEAK 24(12P13.1) WILD-TYPE                               13
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 24(12P13.1) MUTATED                                         3
  DEL PEAK 24(12P13.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 24(12P13.1) MUTATED                             17
  DEL PEAK 24(12P13.1) WILD-TYPE                           27
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 24(12P13.1) MUTATED                                         1
  DEL PEAK 24(12P13.1) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 24(12P13.1) MUTATED                                           2
  DEL PEAK 24(12P13.1) WILD-TYPE                                         0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 24(12P13.1) MUTATED                                                  0
  DEL PEAK 24(12P13.1) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 24(12P13.1) MUTATED                                          3
  DEL PEAK 24(12P13.1) WILD-TYPE                                        5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 24(12P13.1) MUTATED                                                         0
  DEL PEAK 24(12P13.1) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 24(12P13.1) MUTATED                                            0
  DEL PEAK 24(12P13.1) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 24(12P13.1) MUTATED                                                  28
  DEL PEAK 24(12P13.1) WILD-TYPE                                                45
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 24(12P13.1) MUTATED                                                    0
  DEL PEAK 24(12P13.1) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 24(12P13.1) MUTATED                                    1
  DEL PEAK 24(12P13.1) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 24(12P13.1) MUTATED                          1
  DEL PEAK 24(12P13.1) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 24(12P13.1) MUTATED                             2
  DEL PEAK 24(12P13.1) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 24(12P13.1) MUTATED                           0
  DEL PEAK 24(12P13.1) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 24(12P13.1) MUTATED                                   3
  DEL PEAK 24(12P13.1) WILD-TYPE                                 4
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 24(12P13.1) MUTATED                                   3
  DEL PEAK 24(12P13.1) WILD-TYPE                                 2
D49V3, multiclass
                                                         clus
vv                                                        DEL PEAK 24(12P13.1) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             8
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
                                                         clus
vv                                                        DEL PEAK 24(12P13.1) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              20
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    39  48
  DEL PEAK 24(12P13.1) WILD-TYPE 100  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     39   48
  DEL PEAK 24(12P13.1) WILD-TYPE  100   70
        clus
vv       DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  FEMALE                           39                            100
  MALE                             48                             70
[1] 2 2
[1] FALSE
D49V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    60  25
  DEL PEAK 24(12P13.1) WILD-TYPE 119  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     60   25
  DEL PEAK 24(12P13.1) WILD-TYPE  119   47
     clus
vv    DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  NO                            60                            119
  YES                           25                             47
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 24(12P13.1) MUTATED                             20             0
  DEL PEAK 24(12P13.1) WILD-TYPE                           39             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 24(12P13.1) MUTATED                                                                          0
  DEL PEAK 24(12P13.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 24(12P13.1) MUTATED                     33
  DEL PEAK 24(12P13.1) WILD-TYPE                   70
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 24(12P13.1) MUTATED                                                  2
  DEL PEAK 24(12P13.1) WILD-TYPE                                                7
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 24(12P13.1) MUTATED                 10
  DEL PEAK 24(12P13.1) WILD-TYPE               14
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 24(12P13.1) MUTATED                                                         17
  DEL PEAK 24(12P13.1) WILD-TYPE                                                       11
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 24(12P13.1) MUTATED                                          0
  DEL PEAK 24(12P13.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 24(12P13.1) MUTATED                             0
  DEL PEAK 24(12P13.1) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 24(12P13.1) MUTATED                               0
  DEL PEAK 24(12P13.1) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 24(12P13.1) MUTATED                                            5
  DEL PEAK 24(12P13.1) WILD-TYPE                                         16
D49V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 24(12P13.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       20
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               33
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    2
  MYXOFIBROSARCOMA                                                                                   10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          5
                                                                          clus
vv                                                                         DEL PEAK 24(12P13.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         39
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 70
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      7
  MYXOFIBROSARCOMA                                                                                     14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(12P13.1) MUTATED    50  25   4   8
  DEL PEAK 24(12P13.1) WILD-TYPE 102  44   5  18
D49V7, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  R0                           50                            102
  R1                           25                             44
  R2                            4                              5
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12P13.1) MUTATED       1                         7    75
  DEL PEAK 24(12P13.1) WILD-TYPE     5                        11   149
D49V8, multiclass
                           clus
vv                          DEL PEAK 24(12P13.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               75
                           clus
vv                          DEL PEAK 24(12P13.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED     1  76
  DEL PEAK 24(12P13.1) WILD-TYPE   4 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED      1   76
  DEL PEAK 24(12P13.1) WILD-TYPE    4  144
                        clus
vv                       DEL PEAK 24(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       DEL PEAK 24(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 25(12Q12) MUTATION ANALYSIS
D50V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 25(12Q12) MUTATED    28  28
  DEL PEAK 25(12Q12) WILD-TYPE 131  70
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                          56                          201 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                          28                           70 
$`DEL PEAK 25(12Q12) MUTATED`
TCGA-3B-A9HO TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB35 TCGA-HB-A5W3 
       31.53        15.22        14.43        12.07        30.51        12.62 
TCGA-IE-A4EH TCGA-KF-A41W TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HU TCGA-3B-A9HZ 
       26.93        11.70        26.17        35.08        25.25        38.47 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
       18.64        26.56        32.71        54.21        74.66         6.28 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LY TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48R 
        8.58         9.70        33.44        68.55        85.45        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM 
       15.95        31.96         3.06        16.87        21.30        62.20 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-FX-A3NJ 
       38.17        27.95        36.69         6.58        86.10        31.13 
TCGA-HS-A5N7 TCGA-IF-A4AJ TCGA-JV-A5VF TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU 
       33.30        25.22         1.05        23.38        63.81        35.28 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       21.73        14.99        81.01        13.08        17.65        46.82 
TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        8.61        84.79        38.27        65.46        22.62        63.35 
TCGA-X6-A7WD TCGA-X9-A971 
       30.84        27.32 

$`DEL PEAK 25(12Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        34.68        16.18        67.20        34.36        75.32 
TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X 
       17.95        14.07        15.85        40.60       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       22.85       101.98        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       37.02        52.11        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        41.49        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        44.91        54.74        14.37        42.84        10.32 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03         0.56        14.04        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       18.54        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       66.87        27.81        60.30        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD 
       51.02         4.54        14.99        10.68        73.87        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       46.03       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       36.33        28.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EN 
       50.50        86.30        64.21       101.23        34.49        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
       45.14        47.87        40.77       150.35        40.44        60.66 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31        49.15        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        67.63        34.88         4.57         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
      171.09        13.58        85.97         5.92        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       16.41        30.31        25.41         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       38.63         1.84        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       18.94         3.88        22.82        25.35        32.75        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
        8.58        26.43        35.90        18.08        45.34        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                        1.05                         0.49 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                       86.10                       188.15 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                      27.125                       34.360 
[1] "1.1 - 86.1 (27.1)"  "0.5 - 188.2 (34.4)"
[1] "hr=" "1.7"
D50V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 25(12Q12) MUTATED                0                  1
  DEL PEAK 25(12Q12) WILD-TYPE              1                  6
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 25(12Q12) MUTATED                     0                   1
  DEL PEAK 25(12Q12) WILD-TYPE                   2                   0
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 25(12Q12) MUTATED                               0
  DEL PEAK 25(12Q12) WILD-TYPE                             2
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 25(12Q12) MUTATED                       0                      6
  DEL PEAK 25(12Q12) WILD-TYPE                     1                     22
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 25(12Q12) MUTATED                      1                    0
  DEL PEAK 25(12Q12) WILD-TYPE                    1                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 25(12Q12) MUTATED                                       0
  DEL PEAK 25(12Q12) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 25(12Q12) MUTATED                                  0
  DEL PEAK 25(12Q12) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 25(12Q12) MUTATED                                                1
  DEL PEAK 25(12Q12) WILD-TYPE                                              1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 25(12Q12) MUTATED                                 1
  DEL PEAK 25(12Q12) WILD-TYPE                               9
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 25(12Q12) MUTATED                                         0
  DEL PEAK 25(12Q12) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 25(12Q12) MUTATED                              0
  DEL PEAK 25(12Q12) WILD-TYPE                            4
                              vv
clus                           LOWER EXTREMITY - GROIN
  DEL PEAK 25(12Q12) MUTATED                         0
  DEL PEAK 25(12Q12) WILD-TYPE                       2
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 25(12Q12) MUTATED                                  4
  DEL PEAK 25(12Q12) WILD-TYPE                               13
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 25(12Q12) MUTATED                                         1
  DEL PEAK 25(12Q12) WILD-TYPE                                       4
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 25(12Q12) MUTATED                             10
  DEL PEAK 25(12Q12) WILD-TYPE                           34
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 25(12Q12) MUTATED                                         0
  DEL PEAK 25(12Q12) WILD-TYPE                                       4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 25(12Q12) MUTATED                                           1
  DEL PEAK 25(12Q12) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 25(12Q12) MUTATED                                                  1
  DEL PEAK 25(12Q12) WILD-TYPE                                                4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 25(12Q12) MUTATED                                          2
  DEL PEAK 25(12Q12) WILD-TYPE                                        6
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 25(12Q12) MUTATED                                                         0
  DEL PEAK 25(12Q12) WILD-TYPE                                                       2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 25(12Q12) MUTATED                                            0
  DEL PEAK 25(12Q12) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 25(12Q12) MUTATED                                                  19
  DEL PEAK 25(12Q12) WILD-TYPE                                                54
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 25(12Q12) MUTATED                                                    1
  DEL PEAK 25(12Q12) WILD-TYPE                                                  2
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 25(12Q12) MUTATED                                    2
  DEL PEAK 25(12Q12) WILD-TYPE                                  0
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  DEL PEAK 25(12Q12) MUTATED                          0
  DEL PEAK 25(12Q12) WILD-TYPE                        5
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 25(12Q12) MUTATED                             2
  DEL PEAK 25(12Q12) WILD-TYPE                           2
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  DEL PEAK 25(12Q12) MUTATED                           0
  DEL PEAK 25(12Q12) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 25(12Q12) MUTATED                                   2
  DEL PEAK 25(12Q12) WILD-TYPE                                 5
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 25(12Q12) MUTATED                                   0
  DEL PEAK 25(12Q12) WILD-TYPE                                 5
D50V3, multiclass
                                                         clus
vv                                                        DEL PEAK 25(12Q12) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               1
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              1
  CHEST - OTHER (PLEASE SPECIFY                                                    0
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                           6
  HEAD AND NECK - HEAD                                                             1
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     0
  LOWER EXTREMITY - GROIN                                                          0
  LOWER EXTREMITY - LOWER LEG/CALF                                                 4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          1
  LOWER EXTREMITY - THIGH/KNEE                                                    10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               19
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               2
  SUPERFICIAL TRUNK - BACK                                                         0
  SUPERFICIAL TRUNK - BUTTOCK                                                      2
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                0
                                                         clus
vv                                                        DEL PEAK 25(12Q12) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 6
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            22
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       4
  LOWER EXTREMITY - GROIN                                                            2
  LOWER EXTREMITY - LOWER LEG/CALF                                                  13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            4
  LOWER EXTREMITY - THIGH/KNEE                                                      34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 54
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           5
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                              cls
clus                             0   1
  DEL PEAK 25(12Q12) MUTATED    32  24
  DEL PEAK 25(12Q12) WILD-TYPE 107  94
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(12Q12) MUTATED     32   24
  DEL PEAK 25(12Q12) WILD-TYPE  107   94
        clus
vv       DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  FEMALE                         32                          107
  MALE                           24                           94
[1] 2 2
[1] FALSE
D50V5, binary
                              cls
clus                             0   1
  DEL PEAK 25(12Q12) MUTATED    42  13
  DEL PEAK 25(12Q12) WILD-TYPE 137  59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(12Q12) MUTATED     42   13
  DEL PEAK 25(12Q12) WILD-TYPE  137   59
     clus
vv    DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  NO                          42                          137
  YES                         13                           59
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 25(12Q12) MUTATED                             10             0
  DEL PEAK 25(12Q12) WILD-TYPE                           49             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 25(12Q12) MUTATED                                                                          0
  DEL PEAK 25(12Q12) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  DEL PEAK 25(12Q12) MUTATED                     27
  DEL PEAK 25(12Q12) WILD-TYPE                   76
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 25(12Q12) MUTATED                                                  0
  DEL PEAK 25(12Q12) WILD-TYPE                                                9
                              vv
clus                           MYXOFIBROSARCOMA
  DEL PEAK 25(12Q12) MUTATED                  4
  DEL PEAK 25(12Q12) WILD-TYPE               20
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 25(12Q12) MUTATED                                                         10
  DEL PEAK 25(12Q12) WILD-TYPE                                                       18
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 25(12Q12) MUTATED                                          0
  DEL PEAK 25(12Q12) WILD-TYPE                                        2
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 25(12Q12) MUTATED                             0
  DEL PEAK 25(12Q12) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 25(12Q12) MUTATED                               0
  DEL PEAK 25(12Q12) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 25(12Q12) MUTATED                                            5
  DEL PEAK 25(12Q12) WILD-TYPE                                         16
D50V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 25(12Q12) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     10
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  0
  MYXOFIBROSARCOMA                                                                                  4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          0
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        5
                                                                          clus
vv                                                                         DEL PEAK 25(12Q12) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       49
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    9
  MYXOFIBROSARCOMA                                                                                   20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            2
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 25(12Q12) MUTATED    32  17   1   6
  DEL PEAK 25(12Q12) WILD-TYPE 120  52   8  20
D50V7, multiclass
    clus
vv   DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  R0                         32                          120
  R1                         17                           52
  R2                          1                            8
  RX                          6                           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12Q12) MUTATED       0                         8    45
  DEL PEAK 25(12Q12) WILD-TYPE     6                        10   179
D50V8, multiclass
                           clus
vv                          DEL PEAK 25(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          8
  WHITE                                             45
                           clus
vv                          DEL PEAK 25(12Q12) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                              cls
clus                             0   1
  DEL PEAK 25(12Q12) MUTATED     0  50
  DEL PEAK 25(12Q12) WILD-TYPE   5 170
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(12Q12) MUTATED      0   50
  DEL PEAK 25(12Q12) WILD-TYPE    5  170
                        clus
vv                       DEL PEAK 25(12Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         50
                        clus
vv                       DEL PEAK 25(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          170
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 26(12Q24.33) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(12Q24.33) MUTATED    44  26
  DEL PEAK 26(12Q24.33) WILD-TYPE 115  72
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                             70                             187 
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                             26                              72 
$`DEL PEAK 26(12Q24.33) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2H 
       31.53        34.68        34.36        15.22        17.95        15.85 
TCGA-DX-AB2P TCGA-DX-AB35 TCGA-DX-AB3A TCGA-IE-A4EH TCGA-KF-A41W TCGA-PC-A5DM 
       12.07        30.51        32.15        26.93        11.70         6.35 
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW 
       19.69        88.57        38.47        36.03        26.56        32.71 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LY 
       74.66         6.28         8.58         9.70         9.04        33.44 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R 
       14.99        50.43        85.45        45.99        24.26        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A7EI 
       15.95        82.68        31.96        78.28        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-AATS 
       62.20        61.97        47.87        38.17        36.69         1.15 
TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2T TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-HS-A5N8 
       17.79        86.10        77.88        31.13        33.30         0.72 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A42W 
        3.22        19.89        25.22         5.92         1.05        62.17 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V9 
       21.73        14.99       122.96        81.01        13.08        46.82 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 
       37.12         3.88        10.72        84.79        38.27        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X9-A971 TCGA-Z4-AAPG 
       45.34        30.84        27.32        15.98 

$`DEL PEAK 26(12Q24.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        16.18        67.20        75.32        14.43        14.07 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       40.60       106.45        13.28        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK 
       84.66        16.60        37.02        12.62        52.11        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
       28.21       159.29        22.62        17.75         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       50.01        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       14.37        42.84        10.32        18.64         0.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       60.30        95.38        79.17        49.05        86.83       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       44.68        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O 
       73.87        68.55        34.88         9.73        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       46.03       108.82        59.84        37.58        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV 
       28.96        36.85        26.99         3.06        41.00        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EN TCGA-DX-A7EO 
       16.87        86.30        64.21       101.23        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO 
       29.49        48.20        20.05         9.34        45.14        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
      150.35        27.95        40.44        60.66        19.43         6.58 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       12.00        15.72        65.98        66.74         9.21       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       50.40        50.89        71.31        49.15        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.89        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 
        9.80        80.48        19.53         1.38        37.12       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        85.97        16.41         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       35.28        30.31        25.41         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        11.57        10.45         7.36        37.55        38.63 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD 
       17.65         1.84        18.08        48.59        35.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       22.82        25.35        32.75         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 
       13.41        12.46        11.93         4.80        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C3 
        8.58        63.35        35.90        18.08        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       20.65        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                           0.72                            0.49 
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                         122.96                          188.15 
  DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE 
                         30.675                          32.750 
[1] "0.7 - 123.0 (30.7)" "0.5 - 188.2 (32.8)"
[1] "hr=" "1.1"
D51V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 26(12Q24.33) MUTATED                0                  1
  DEL PEAK 26(12Q24.33) WILD-TYPE              1                  6
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 26(12Q24.33) MUTATED                     0                   1
  DEL PEAK 26(12Q24.33) WILD-TYPE                   2                   0
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 26(12Q24.33) MUTATED                               0
  DEL PEAK 26(12Q24.33) WILD-TYPE                             2
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 26(12Q24.33) MUTATED                       0                      4
  DEL PEAK 26(12Q24.33) WILD-TYPE                     1                     24
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 26(12Q24.33) MUTATED                      1                    0
  DEL PEAK 26(12Q24.33) WILD-TYPE                    1                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 26(12Q24.33) MUTATED                                       0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 26(12Q24.33) MUTATED                                  0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 26(12Q24.33) MUTATED                                                2
  DEL PEAK 26(12Q24.33) WILD-TYPE                                              0
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 26(12Q24.33) MUTATED                                 2
  DEL PEAK 26(12Q24.33) WILD-TYPE                               8
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 26(12Q24.33) MUTATED                                         0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 26(12Q24.33) MUTATED                              1
  DEL PEAK 26(12Q24.33) WILD-TYPE                            3
                                 vv
clus                              LOWER EXTREMITY - GROIN
  DEL PEAK 26(12Q24.33) MUTATED                         0
  DEL PEAK 26(12Q24.33) WILD-TYPE                       2
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 26(12Q24.33) MUTATED                                  5
  DEL PEAK 26(12Q24.33) WILD-TYPE                               12
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 26(12Q24.33) MUTATED                                         3
  DEL PEAK 26(12Q24.33) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 26(12Q24.33) MUTATED                             13
  DEL PEAK 26(12Q24.33) WILD-TYPE                           31
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 26(12Q24.33) MUTATED                                         0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                       4
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 26(12Q24.33) MUTATED                                           1
  DEL PEAK 26(12Q24.33) WILD-TYPE                                         1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 26(12Q24.33) MUTATED                                                  1
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                4
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 26(12Q24.33) MUTATED                                          3
  DEL PEAK 26(12Q24.33) WILD-TYPE                                        5
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 26(12Q24.33) MUTATED                                                         0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                       2
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 26(12Q24.33) MUTATED                                            1
  DEL PEAK 26(12Q24.33) WILD-TYPE                                          0
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 26(12Q24.33) MUTATED                                                  26
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                47
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 26(12Q24.33) MUTATED                                                    0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                  3
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 26(12Q24.33) MUTATED                                    1
  DEL PEAK 26(12Q24.33) WILD-TYPE                                  1
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  DEL PEAK 26(12Q24.33) MUTATED                          0
  DEL PEAK 26(12Q24.33) WILD-TYPE                        5
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 26(12Q24.33) MUTATED                             1
  DEL PEAK 26(12Q24.33) WILD-TYPE                           3
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  DEL PEAK 26(12Q24.33) MUTATED                           0
  DEL PEAK 26(12Q24.33) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 26(12Q24.33) MUTATED                                   3
  DEL PEAK 26(12Q24.33) WILD-TYPE                                 4
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 26(12Q24.33) MUTATED                                   0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                 5
D51V3, multiclass
                                                         clus
vv                                                        DEL PEAK 26(12Q24.33) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  1
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       0
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                              4
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        1
  LOWER EXTREMITY - GROIN                                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                                    5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  26
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            0
  SUPERFICIAL TRUNK - BUTTOCK                                                         1
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   0
                                                         clus
vv                                                        DEL PEAK 26(12Q24.33) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    6
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                                         2
  GYNECOLOGICAL - OVARY                                                                 1
  GYNECOLOGICAL - UTERUS                                                               24
  HEAD AND NECK - HEAD                                                                  1
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          3
  LOWER EXTREMITY - GROIN                                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               2
  LOWER EXTREMITY - THIGH/KNEE                                                         31
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    47
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    1
  SUPERFICIAL TRUNK - BACK                                                              5
  SUPERFICIAL TRUNK - BUTTOCK                                                           3
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                                 cls
clus                                0   1
  DEL PEAK 26(12Q24.33) MUTATED    32  38
  DEL PEAK 26(12Q24.33) WILD-TYPE 107  80
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(12Q24.33) MUTATED     32   38
  DEL PEAK 26(12Q24.33) WILD-TYPE  107   80
        clus
vv       DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE
  FEMALE                            32                             107
  MALE                              38                              80
[1] 2 2
[1] FALSE
D51V5, binary
                                 cls
clus                                0   1
  DEL PEAK 26(12Q24.33) MUTATED    50  18
  DEL PEAK 26(12Q24.33) WILD-TYPE 129  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(12Q24.33) MUTATED     50   18
  DEL PEAK 26(12Q24.33) WILD-TYPE  129   54
     clus
vv    DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE
  NO                             50                             129
  YES                            18                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 26(12Q24.33) MUTATED                             16             0
  DEL PEAK 26(12Q24.33) WILD-TYPE                           43             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 26(12Q24.33) MUTATED                                                                          0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  DEL PEAK 26(12Q24.33) MUTATED                     32
  DEL PEAK 26(12Q24.33) WILD-TYPE                   71
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 26(12Q24.33) MUTATED                                                  0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                9
                                 vv
clus                              MYXOFIBROSARCOMA
  DEL PEAK 26(12Q24.33) MUTATED                  6
  DEL PEAK 26(12Q24.33) WILD-TYPE               18
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 26(12Q24.33) MUTATED                                                         11
  DEL PEAK 26(12Q24.33) WILD-TYPE                                                       17
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 26(12Q24.33) MUTATED                                          0
  DEL PEAK 26(12Q24.33) WILD-TYPE                                        2
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 26(12Q24.33) MUTATED                             0
  DEL PEAK 26(12Q24.33) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 26(12Q24.33) MUTATED                               0
  DEL PEAK 26(12Q24.33) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 26(12Q24.33) MUTATED                                            5
  DEL PEAK 26(12Q24.33) WILD-TYPE                                         16
D51V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 26(12Q24.33) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        16
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     0
  MYXOFIBROSARCOMA                                                                                     6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           5
                                                                          clus
vv                                                                         DEL PEAK 26(12Q24.33) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          43
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       9
  MYXOFIBROSARCOMA                                                                                      18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(12Q24.33) MUTATED    42  22   2   4
  DEL PEAK 26(12Q24.33) WILD-TYPE 110  47   7  22
D51V7, multiclass
    clus
vv   DEL PEAK 26(12Q24.33) MUTATED DEL PEAK 26(12Q24.33) WILD-TYPE
  R0                            42                             110
  R1                            22                              47
  R2                             2                               7
  RX                             4                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(12Q24.33) MUTATED       0                         5    63
  DEL PEAK 26(12Q24.33) WILD-TYPE     6                        13   161
D51V8, multiclass
                           clus
vv                          DEL PEAK 26(12Q24.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                63
                           clus
vv                          DEL PEAK 26(12Q24.33) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              13
  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"
D51V9, binary
                                 cls
clus                                0   1
  DEL PEAK 26(12Q24.33) MUTATED     0  62
  DEL PEAK 26(12Q24.33) WILD-TYPE   5 158
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(12Q24.33) MUTATED      0   62
  DEL PEAK 26(12Q24.33) WILD-TYPE    5  158
                        clus
vv                       DEL PEAK 26(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            62
                        clus
vv                       DEL PEAK 26(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             158
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 27(13Q14.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(13Q14.2) MUTATED   110  70
  DEL PEAK 27(13Q14.2) WILD-TYPE  49  28
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                           180                             77 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                            70                             28 
$`DEL PEAK 27(13Q14.2) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG 
       16.18        67.20        34.36        75.32        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 
       14.43        14.07        12.07       106.45       101.98        30.51 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       16.60        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       28.21        22.62        11.70        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
       18.08        20.94       188.15        17.52        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       50.01        19.69        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56         0.56        14.04        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       45.11        18.54        54.21        74.66         6.28         9.70 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 
        9.04        49.05        33.44        44.68        51.02        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ 
       37.58        15.95        82.68        36.33        31.96         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        16.87        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       21.30        62.20        30.35         9.34        61.97        45.14 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        40.77       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q 
       60.66         1.15        17.79        12.00        86.10        66.74 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ 
       77.88       106.55        50.40        50.89        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3L4 
       21.70        20.32        19.89        15.48        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        85.97        16.41         1.05         3.91       101.26 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       62.17        23.38         5.19        63.81        16.41        35.28 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA 
       25.41         0.49        21.73        19.73        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
      122.96        37.55        81.01        13.08        17.65        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 
       18.08        48.59        35.90        10.52        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G 
        3.88        22.82        25.35         8.61        19.63        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93        84.79        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        8.58        63.35        26.43        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 
       30.84        35.18        19.17        20.65        50.86        27.32 

$`DEL PEAK 27(13Q14.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X 
       36.30        31.53        34.68        15.85        40.60        13.28 
TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-IS-A3K8 TCGA-WK-A8XT 
       22.85        60.00        84.66        32.15       159.29        41.49 
TCGA-3B-A9HP TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       53.49        32.71        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         8.58        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       79.17        86.83       136.44        31.86        35.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG 
       10.68        73.87        35.28        37.41        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       26.99        50.50        34.49       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2L 
       20.05        47.87        19.43         6.58        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-K1-A42X 
        9.21        71.31         8.05         5.92        53.33       123.78 
TCGA-K1-A6RT TCGA-LI-A67I TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       17.36        30.31        14.99        17.98        22.39        11.57 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       38.63         1.84        37.12       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-X6-A8C7 
        0.72        32.75        13.22        13.41         4.80        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                          0.49                           0.72 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                         28.08                          32.75 
[1] "0.5 - 188.2 (28.1)" "0.7 - 159.3 (32.8)"
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 27(13Q14.2) MUTATED                1                  5
  DEL PEAK 27(13Q14.2) WILD-TYPE              0                  2
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 27(13Q14.2) MUTATED                     0                   1
  DEL PEAK 27(13Q14.2) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 27(13Q14.2) MUTATED                               2
  DEL PEAK 27(13Q14.2) WILD-TYPE                             0
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 27(13Q14.2) MUTATED                       1                     25
  DEL PEAK 27(13Q14.2) WILD-TYPE                     0                      3
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 27(13Q14.2) MUTATED                      1                    0
  DEL PEAK 27(13Q14.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 27(13Q14.2) MUTATED                                       1
  DEL PEAK 27(13Q14.2) WILD-TYPE                                     1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 27(13Q14.2) MUTATED                                  0
  DEL PEAK 27(13Q14.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 27(13Q14.2) MUTATED                                                1
  DEL PEAK 27(13Q14.2) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 27(13Q14.2) MUTATED                                 5
  DEL PEAK 27(13Q14.2) WILD-TYPE                               5
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 27(13Q14.2) MUTATED                                         0
  DEL PEAK 27(13Q14.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 27(13Q14.2) MUTATED                              1
  DEL PEAK 27(13Q14.2) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 27(13Q14.2) MUTATED                         1
  DEL PEAK 27(13Q14.2) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 27(13Q14.2) MUTATED                                 14
  DEL PEAK 27(13Q14.2) WILD-TYPE                                3
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 27(13Q14.2) MUTATED                                         5
  DEL PEAK 27(13Q14.2) WILD-TYPE                                       0
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 27(13Q14.2) MUTATED                             34
  DEL PEAK 27(13Q14.2) WILD-TYPE                           10
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 27(13Q14.2) MUTATED                                         3
  DEL PEAK 27(13Q14.2) WILD-TYPE                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 27(13Q14.2) MUTATED                                           2
  DEL PEAK 27(13Q14.2) WILD-TYPE                                         0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 27(13Q14.2) MUTATED                                                  1
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 27(13Q14.2) MUTATED                                          6
  DEL PEAK 27(13Q14.2) WILD-TYPE                                        2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 27(13Q14.2) MUTATED                                                         2
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                       0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 27(13Q14.2) MUTATED                                            1
  DEL PEAK 27(13Q14.2) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 27(13Q14.2) MUTATED                                                  46
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                27
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 27(13Q14.2) MUTATED                                                    2
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 27(13Q14.2) MUTATED                                    2
  DEL PEAK 27(13Q14.2) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 27(13Q14.2) MUTATED                          3
  DEL PEAK 27(13Q14.2) WILD-TYPE                        2
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 27(13Q14.2) MUTATED                             3
  DEL PEAK 27(13Q14.2) WILD-TYPE                           1
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 27(13Q14.2) MUTATED                           0
  DEL PEAK 27(13Q14.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 27(13Q14.2) MUTATED                                   6
  DEL PEAK 27(13Q14.2) WILD-TYPE                                 1
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 27(13Q14.2) MUTATED                                   4
  DEL PEAK 27(13Q14.2) WILD-TYPE                                 1
D52V3, multiclass
                                                         clus
vv                                                        DEL PEAK 27(13Q14.2) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 5
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      2
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            25
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            5
  LOWER EXTREMITY - THIGH/KNEE                                                      34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           3
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  4
                                                         clus
vv                                                        DEL PEAK 27(13Q14.2) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   2
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        0
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                               3
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              0
  LOWER EXTREMITY - THIGH/KNEE                                                        10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             2
  SUPERFICIAL TRUNK - BUTTOCK                                                          1
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q14.2) MUTATED   104  76
  DEL PEAK 27(13Q14.2) WILD-TYPE  35  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q14.2) MUTATED    104   76
  DEL PEAK 27(13Q14.2) WILD-TYPE   35   42
        clus
vv       DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  FEMALE                          104                             35
  MALE                             76                             42
[1] 2 2
[1] FALSE
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q14.2) MUTATED   117  58
  DEL PEAK 27(13Q14.2) WILD-TYPE  62  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q14.2) MUTATED    117   58
  DEL PEAK 27(13Q14.2) WILD-TYPE   62   14
     clus
vv    DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  NO                           117                             62
  YES                           58                             14
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 27(13Q14.2) MUTATED                             26             0
  DEL PEAK 27(13Q14.2) WILD-TYPE                           33             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 27(13Q14.2) MUTATED                                                                          0
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 27(13Q14.2) MUTATED                     88
  DEL PEAK 27(13Q14.2) WILD-TYPE                   15
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 27(13Q14.2) MUTATED                                                  6
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                3
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 27(13Q14.2) MUTATED                 18
  DEL PEAK 27(13Q14.2) WILD-TYPE                6
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 27(13Q14.2) MUTATED                                                         24
  DEL PEAK 27(13Q14.2) WILD-TYPE                                                        4
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 27(13Q14.2) MUTATED                                          0
  DEL PEAK 27(13Q14.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 27(13Q14.2) MUTATED                             0
  DEL PEAK 27(13Q14.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 27(13Q14.2) MUTATED                               1
  DEL PEAK 27(13Q14.2) WILD-TYPE                             5
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 27(13Q14.2) MUTATED                                           17
  DEL PEAK 27(13Q14.2) WILD-TYPE                                          4
D52V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 27(13Q14.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       26
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    6
  MYXOFIBROSARCOMA                                                                                   18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           24
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         17
                                                                          clus
vv                                                                         DEL PEAK 27(13Q14.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         33
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      3
  MYXOFIBROSARCOMA                                                                                      6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(13Q14.2) MUTATED   105  47   8  19
  DEL PEAK 27(13Q14.2) WILD-TYPE  47  22   1   7
D52V7, multiclass
    clus
vv   DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  R0                          105                             47
  R1                           47                             22
  R2                            8                              1
  RX                           19                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(13Q14.2) MUTATED       3                        13   156
  DEL PEAK 27(13Q14.2) WILD-TYPE     3                         5    68
D52V8, multiclass
                           clus
vv                          DEL PEAK 27(13Q14.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              156
                           clus
vv                          DEL PEAK 27(13Q14.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q14.2) MUTATED     2 157
  DEL PEAK 27(13Q14.2) WILD-TYPE   3  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q14.2) MUTATED      2  157
  DEL PEAK 27(13Q14.2) WILD-TYPE    3   63
                        clus
vv                       DEL PEAK 27(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          157
                        clus
vv                       DEL PEAK 27(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             63
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 28(14Q24.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(14Q24.1) MUTATED    50  30
  DEL PEAK 28(14Q24.1) WILD-TYPE 109  68
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            80                            177 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            30                             68 
$`DEL PEAK 28(14Q24.1) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 
       34.68        34.36        12.07       101.98        30.51        84.66 
TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       37.02        26.93        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 
       17.75        19.69        53.49        14.37        42.84        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       26.56        14.04        32.71        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       18.54        74.66        49.05        86.83        33.44        31.86 
TCGA-DX-A3UE TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 
       34.88        35.28        52.77        46.03       108.82        37.58 
TCGA-DX-A6B8 TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A8BM TCGA-DX-A8BN 
       15.95        86.30        64.21       101.23        47.87        38.17 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2T 
       40.44        36.69        60.66         6.58        86.10        77.88 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 
       49.15        31.13        21.70        19.89        15.48        34.88 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE 
        0.72         9.80         3.22       171.09        85.97        16.41 
TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 
        1.05       123.78        23.38        63.81        35.28        25.41 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P 
       13.08        17.65        46.82        10.52        16.77        25.35 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC 
        8.61        10.72         8.58        63.35        18.08        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C5 
       35.18        50.86 

$`DEL PEAK 28(14Q24.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       17.95        14.43        14.07        15.85        40.60       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 
       13.28        22.85        60.00        32.15        16.60        12.62 
TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX 
       52.11        52.27         8.28         6.35        18.08        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
      188.15        17.52        26.17        41.49        35.08        50.01 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       68.55        88.57        44.91        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.47        36.03         0.56        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       66.94         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
      136.44        44.68        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        73.87        68.55        50.43        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       45.99        24.26        26.47        59.84        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI 
       41.00        78.28        50.50        16.87        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
        9.34        61.97        45.14        40.77       150.35        27.95 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       66.74         9.21       106.55        50.40        50.89        71.31 
TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A3OV 
       20.32         8.05        67.63         4.57        33.30        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
       19.53         1.38        19.89        37.12        25.22        13.58 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
        5.92         3.91       101.26        53.33        62.17        17.36 
TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
        5.19        16.41        30.31         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA 
      122.96        37.55        38.63        81.01         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C 
        0.72        18.94         3.88        22.82        32.75        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22        13.41        12.46        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD 
       38.27        65.46        22.62        26.43        35.90        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                        171.09                         188.15 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                         34.52                          29.46 
[1] "0.7 - 171.1 (34.5)" "0.5 - 188.2 (29.5)"
[1] "hr=" "1.1"
D53V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 28(14Q24.1) MUTATED                0                  2
  DEL PEAK 28(14Q24.1) WILD-TYPE              1                  5
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 28(14Q24.1) MUTATED                     0                   0
  DEL PEAK 28(14Q24.1) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 28(14Q24.1) MUTATED                               1
  DEL PEAK 28(14Q24.1) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 28(14Q24.1) MUTATED                       1                     21
  DEL PEAK 28(14Q24.1) WILD-TYPE                     0                      7
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 28(14Q24.1) MUTATED                      1                    0
  DEL PEAK 28(14Q24.1) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 28(14Q24.1) MUTATED                                       0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 28(14Q24.1) MUTATED                                  0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 28(14Q24.1) MUTATED                                                0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 28(14Q24.1) MUTATED                                 3
  DEL PEAK 28(14Q24.1) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 28(14Q24.1) MUTATED                                         0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 28(14Q24.1) MUTATED                              0
  DEL PEAK 28(14Q24.1) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 28(14Q24.1) MUTATED                         0
  DEL PEAK 28(14Q24.1) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 28(14Q24.1) MUTATED                                  4
  DEL PEAK 28(14Q24.1) WILD-TYPE                               13
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 28(14Q24.1) MUTATED                                         1
  DEL PEAK 28(14Q24.1) WILD-TYPE                                       4
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 28(14Q24.1) MUTATED                             12
  DEL PEAK 28(14Q24.1) WILD-TYPE                           32
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 28(14Q24.1) MUTATED                                         2
  DEL PEAK 28(14Q24.1) WILD-TYPE                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 28(14Q24.1) MUTATED                                           0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 28(14Q24.1) MUTATED                                                  0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 28(14Q24.1) MUTATED                                          1
  DEL PEAK 28(14Q24.1) WILD-TYPE                                        7
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 28(14Q24.1) MUTATED                                                         1
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 28(14Q24.1) MUTATED                                            0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 28(14Q24.1) MUTATED                                                  21
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                52
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 28(14Q24.1) MUTATED                                                    1
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                  2
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 28(14Q24.1) MUTATED                                    0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 28(14Q24.1) MUTATED                          1
  DEL PEAK 28(14Q24.1) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 28(14Q24.1) MUTATED                             2
  DEL PEAK 28(14Q24.1) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 28(14Q24.1) MUTATED                           0
  DEL PEAK 28(14Q24.1) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 28(14Q24.1) MUTATED                                   3
  DEL PEAK 28(14Q24.1) WILD-TYPE                                 4
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 28(14Q24.1) MUTATED                                   1
  DEL PEAK 28(14Q24.1) WILD-TYPE                                 4
D53V3, multiclass
                                                         clus
vv                                                        DEL PEAK 28(14Q24.1) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            21
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            1
  LOWER EXTREMITY - THIGH/KNEE                                                      12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        DEL PEAK 28(14Q24.1) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   5
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                               7
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              4
  LOWER EXTREMITY - THIGH/KNEE                                                        32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   52
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                                cls
clus                              0  1
  DEL PEAK 28(14Q24.1) MUTATED   49 31
  DEL PEAK 28(14Q24.1) WILD-TYPE 90 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q24.1) MUTATED     49   31
  DEL PEAK 28(14Q24.1) WILD-TYPE   90   87
        clus
vv       DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  FEMALE                           49                             90
  MALE                             31                             87
[1] 2 2
[1] FALSE
D53V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q24.1) MUTATED    52  25
  DEL PEAK 28(14Q24.1) WILD-TYPE 127  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q24.1) MUTATED     52   25
  DEL PEAK 28(14Q24.1) WILD-TYPE  127   47
     clus
vv    DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  NO                            52                            127
  YES                           25                             47
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 28(14Q24.1) MUTATED                             17             0
  DEL PEAK 28(14Q24.1) WILD-TYPE                           42             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 28(14Q24.1) MUTATED                                                                          0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 28(14Q24.1) MUTATED                     38
  DEL PEAK 28(14Q24.1) WILD-TYPE                   65
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 28(14Q24.1) MUTATED                                                  3
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 28(14Q24.1) MUTATED                  7
  DEL PEAK 28(14Q24.1) WILD-TYPE               17
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 28(14Q24.1) MUTATED                                                          8
  DEL PEAK 28(14Q24.1) WILD-TYPE                                                       20
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 28(14Q24.1) MUTATED                                          0
  DEL PEAK 28(14Q24.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 28(14Q24.1) MUTATED                             0
  DEL PEAK 28(14Q24.1) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 28(14Q24.1) MUTATED                               0
  DEL PEAK 28(14Q24.1) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 28(14Q24.1) MUTATED                                            7
  DEL PEAK 28(14Q24.1) WILD-TYPE                                         14
D53V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 28(14Q24.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       17
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               38
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                    7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          7
                                                                          clus
vv                                                                         DEL PEAK 28(14Q24.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         42
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 65
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(14Q24.1) MUTATED    41  21   5  12
  DEL PEAK 28(14Q24.1) WILD-TYPE 111  48   4  14
D53V7, multiclass
    clus
vv   DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  R0                           41                            111
  R1                           21                             48
  R2                            5                              4
  RX                           12                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(14Q24.1) MUTATED       1                         7    70
  DEL PEAK 28(14Q24.1) WILD-TYPE     5                        11   154
D53V8, multiclass
                           clus
vv                          DEL PEAK 28(14Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               70
                           clus
vv                          DEL PEAK 28(14Q24.1) WILD-TYPE
  ASIAN                                                  5
  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"
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q24.1) MUTATED     0  68
  DEL PEAK 28(14Q24.1) WILD-TYPE   5 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q24.1) MUTATED      0   68
  DEL PEAK 28(14Q24.1) WILD-TYPE    5  152
                        clus
vv                       DEL PEAK 28(14Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 28(14Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            152
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 29(15Q11.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(15Q11.2) MUTATED    23  24
  DEL PEAK 29(15Q11.2) WILD-TYPE 136  74
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            47                            210 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            24                             74 
$`DEL PEAK 29(15Q11.2) MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB37 TCGA-DX-AB3A TCGA-LI-A9QH TCGA-PC-A5DM 
       15.22        14.43        84.66        32.15        17.75         6.35 
TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HV TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A3LS 
       17.52        50.01        14.37         0.56        14.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48O TCGA-DX-A6B8 TCGA-DX-A6BF 
       49.05        10.68        73.87        52.77        15.95        31.96 
TCGA-DX-A6YQ TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BM TCGA-DX-A8BO 
        3.06        86.30        21.30        34.49        47.87        40.77 
TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IE-A4EJ 
       27.95        60.66         6.58        49.15        67.63         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       19.89        37.12       171.09        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KD-A5QU TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VA 
        1.05         5.19        35.28        13.08        17.65        18.08 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X9-A971 
       12.46        22.62        26.43        35.18        27.32 

$`DEL PEAK 29(15Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        17.95        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       16.60        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP 
       28.21       159.29        22.62        11.70         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL 
       20.94       188.15        26.17        41.49        35.08        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       95.38        79.17        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC 
       31.86        35.77        51.02         4.54        14.99        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       35.28        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        82.68        36.33        28.96        36.85        26.99 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        50.50        16.87        64.21       101.23 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT 
        9.34        61.97        45.14        38.17       150.35        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        19.43         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       65.98        86.10        66.74         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.40        50.89        71.31        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       19.89        15.48         8.05        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
        0.72         9.80        80.48        19.53         1.38        25.22 
TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       13.58         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
       17.36        23.38        63.81        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01         1.84        46.82        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        10.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        38.27        65.46         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        30.84        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        36.43         4.37        13.38        15.95        15.98 

  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                          0.56                           0.49 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                        171.09                         188.15 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                        21.300                         33.025 
[1] "0.6 - 171.1 (21.3)" "0.5 - 188.2 (33.0)"
[1] "hr=" "1.8"
D54V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 29(15Q11.2) MUTATED                0                  1
  DEL PEAK 29(15Q11.2) WILD-TYPE              1                  6
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 29(15Q11.2) MUTATED                     0                   0
  DEL PEAK 29(15Q11.2) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 29(15Q11.2) MUTATED                               0
  DEL PEAK 29(15Q11.2) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 29(15Q11.2) MUTATED                       0                      5
  DEL PEAK 29(15Q11.2) WILD-TYPE                     1                     23
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 29(15Q11.2) MUTATED                      1                    0
  DEL PEAK 29(15Q11.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 29(15Q11.2) MUTATED                                       0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 29(15Q11.2) MUTATED                                  0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 29(15Q11.2) MUTATED                                                0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 29(15Q11.2) MUTATED                                 2
  DEL PEAK 29(15Q11.2) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 29(15Q11.2) MUTATED                                         0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 29(15Q11.2) MUTATED                              1
  DEL PEAK 29(15Q11.2) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 29(15Q11.2) MUTATED                         0
  DEL PEAK 29(15Q11.2) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 29(15Q11.2) MUTATED                                  3
  DEL PEAK 29(15Q11.2) WILD-TYPE                               14
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 29(15Q11.2) MUTATED                                         2
  DEL PEAK 29(15Q11.2) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 29(15Q11.2) MUTATED                              9
  DEL PEAK 29(15Q11.2) WILD-TYPE                           35
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 29(15Q11.2) MUTATED                                         0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 29(15Q11.2) MUTATED                                           0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 29(15Q11.2) MUTATED                                                  0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 29(15Q11.2) MUTATED                                          0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                        8
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 29(15Q11.2) MUTATED                                                         1
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 29(15Q11.2) MUTATED                                            0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 29(15Q11.2) MUTATED                                                  10
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                63
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 29(15Q11.2) MUTATED                                                    1
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                  2
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 29(15Q11.2) MUTATED                                    2
  DEL PEAK 29(15Q11.2) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 29(15Q11.2) MUTATED                          0
  DEL PEAK 29(15Q11.2) WILD-TYPE                        5
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 29(15Q11.2) MUTATED                             3
  DEL PEAK 29(15Q11.2) WILD-TYPE                           1
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 29(15Q11.2) MUTATED                           0
  DEL PEAK 29(15Q11.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 29(15Q11.2) MUTATED                                   2
  DEL PEAK 29(15Q11.2) WILD-TYPE                                 5
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 29(15Q11.2) MUTATED                                   4
  DEL PEAK 29(15Q11.2) WILD-TYPE                                 1
D54V3, multiclass
                                                         clus
vv                                                        DEL PEAK 29(15Q11.2) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 1
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             5
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                       9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 10
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  4
                                                         clus
vv                                                        DEL PEAK 29(15Q11.2) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   6
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              23
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   63
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                                          1
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED    28  19
  DEL PEAK 29(15Q11.2) WILD-TYPE 111  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED     28   19
  DEL PEAK 29(15Q11.2) WILD-TYPE  111   99
        clus
vv       DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  FEMALE                           28                            111
  MALE                             19                             99
[1] 2 2
[1] FALSE
D54V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED    29  17
  DEL PEAK 29(15Q11.2) WILD-TYPE 150  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED     29   17
  DEL PEAK 29(15Q11.2) WILD-TYPE  150   55
     clus
vv    DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  NO                            29                            150
  YES                           17                             55
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 29(15Q11.2) MUTATED                             12             0
  DEL PEAK 29(15Q11.2) WILD-TYPE                           47             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 29(15Q11.2) MUTATED                                                                          0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 29(15Q11.2) MUTATED                     15
  DEL PEAK 29(15Q11.2) WILD-TYPE                   88
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 29(15Q11.2) MUTATED                                                  0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                9
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 29(15Q11.2) MUTATED                  4
  DEL PEAK 29(15Q11.2) WILD-TYPE               20
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 29(15Q11.2) MUTATED                                                          8
  DEL PEAK 29(15Q11.2) WILD-TYPE                                                       20
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 29(15Q11.2) MUTATED                                          0
  DEL PEAK 29(15Q11.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 29(15Q11.2) MUTATED                             0
  DEL PEAK 29(15Q11.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 29(15Q11.2) MUTATED                               0
  DEL PEAK 29(15Q11.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 29(15Q11.2) MUTATED                                            8
  DEL PEAK 29(15Q11.2) WILD-TYPE                                         13
D54V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 29(15Q11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       12
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    0
  MYXOFIBROSARCOMA                                                                                    4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          8
                                                                          clus
vv                                                                         DEL PEAK 29(15Q11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         47
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      9
  MYXOFIBROSARCOMA                                                                                     20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(15Q11.2) MUTATED    28  11   4   4
  DEL PEAK 29(15Q11.2) WILD-TYPE 124  58   5  22
D54V7, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  R0                           28                            124
  R1                           11                             58
  R2                            4                              5
  RX                            4                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(15Q11.2) MUTATED       0                         7    38
  DEL PEAK 29(15Q11.2) WILD-TYPE     6                        11   186
D54V8, multiclass
                           clus
vv                          DEL PEAK 29(15Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               38
                           clus
vv                          DEL PEAK 29(15Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             11
  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"
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED     0  41
  DEL PEAK 29(15Q11.2) WILD-TYPE   5 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED      0   41
  DEL PEAK 29(15Q11.2) WILD-TYPE    5  179
                        clus
vv                       DEL PEAK 29(15Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK 29(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 30(16Q11.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(16Q11.2) MUTATED   82 48
  DEL PEAK 30(16Q11.2) WILD-TYPE 77 50
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                           130                            127 
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                            48                             50 
$`DEL PEAK 30(16Q11.2) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP 
       31.53        67.20        34.36        15.22        17.95        14.07 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-HB-A43Z 
       40.60        12.07       106.45        13.28       101.98        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DP 
       12.62        26.93        52.27        11.70         6.35        18.08 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94        17.52        26.17        35.08        50.01        19.69 
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 
       88.57        25.25        10.32        38.47        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT 
        0.56        18.54        74.66         6.28         9.70        49.05 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       33.44        31.86        51.02        14.99        10.68        68.55 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       50.43        85.45        45.99        24.26        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YX 
       26.47        59.84        15.95        82.68        36.33        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A8BJ TCGA-DX-A8BK 
       86.30        64.21        62.20       152.12         9.34        61.97 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ 
       40.77       150.35        27.95        40.44        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-FX-A3NJ 
        1.15        12.00        66.74        77.88        50.40        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
       21.70        20.32        19.89        15.48        67.63         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72         9.80        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.89        37.12        25.22        13.58        85.97        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QT 
        1.05         3.91       101.26       123.78         5.19        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA 
       35.28        25.41        21.73        19.73        14.99         7.36 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       37.55        81.01        13.08        17.65        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B 
       35.90        37.12        16.77        18.94        22.82         8.61 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       19.63        13.41        12.46        84.79        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A973 TCGA-Z4-AAPG 
       20.65        50.86        36.43        15.98 

$`DEL PEAK 30(16Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-AB2H 
       36.30        34.68        16.18        75.32        14.43        15.85 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       22.85        30.51        60.00        84.66        32.15        16.60 
TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.11        28.21       159.29        22.62        17.75         8.28 
TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
      188.15        41.49        53.49        68.55        44.91        54.74 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       14.37        42.84        36.03        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        45.11        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       95.38        79.17         9.04        86.83       136.44        44.68 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N 
       35.77         4.54        73.87        34.88         9.73        35.28 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
      108.82        37.58        37.41        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z2 
       26.99         3.06        41.00        78.28        50.50       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       21.30        34.49        30.35        29.49        48.20        20.05 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E 
       45.14        47.87        38.17        60.66        19.43        17.79 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B 
       15.72        65.98        86.10         9.21       106.55        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-IE-A3OV TCGA-IS-A3K7 
       71.31        49.15         8.05        34.88        80.48       171.09 
TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS 
        5.92        53.33        62.17        17.36        23.38        63.81 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       30.31         0.49        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF 
      122.96        38.63         1.84        18.08       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
       64.77        10.52         0.72         3.88        25.35        32.75 
TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       13.22        10.72        11.93         4.80        22.62         8.58 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       45.34        19.17        29.46        27.32         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                          0.56                           0.49 
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                        152.12                         188.15 
  DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE 
                         26.45                          34.49 
[1] "0.6 - 152.1 (26.4)" "0.5 - 188.2 (34.5)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 30(16Q11.2) MUTATED                1                  3
  DEL PEAK 30(16Q11.2) WILD-TYPE              0                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 30(16Q11.2) MUTATED                     0                   1
  DEL PEAK 30(16Q11.2) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 30(16Q11.2) MUTATED                               1
  DEL PEAK 30(16Q11.2) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 30(16Q11.2) MUTATED                       1                     18
  DEL PEAK 30(16Q11.2) WILD-TYPE                     0                     10
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 30(16Q11.2) MUTATED                      1                    0
  DEL PEAK 30(16Q11.2) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 30(16Q11.2) MUTATED                                       0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 30(16Q11.2) MUTATED                                  0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 30(16Q11.2) MUTATED                                                2
  DEL PEAK 30(16Q11.2) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 30(16Q11.2) MUTATED                                 6
  DEL PEAK 30(16Q11.2) WILD-TYPE                               4
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 30(16Q11.2) MUTATED                                         0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 30(16Q11.2) MUTATED                              2
  DEL PEAK 30(16Q11.2) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 30(16Q11.2) MUTATED                         1
  DEL PEAK 30(16Q11.2) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 30(16Q11.2) MUTATED                                 11
  DEL PEAK 30(16Q11.2) WILD-TYPE                                6
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 30(16Q11.2) MUTATED                                         2
  DEL PEAK 30(16Q11.2) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 30(16Q11.2) MUTATED                             29
  DEL PEAK 30(16Q11.2) WILD-TYPE                           15
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 30(16Q11.2) MUTATED                                         0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 30(16Q11.2) MUTATED                                           1
  DEL PEAK 30(16Q11.2) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 30(16Q11.2) MUTATED                                                  1
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 30(16Q11.2) MUTATED                                          5
  DEL PEAK 30(16Q11.2) WILD-TYPE                                        3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 30(16Q11.2) MUTATED                                                         0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 30(16Q11.2) MUTATED                                            0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 30(16Q11.2) MUTATED                                                  28
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                45
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 30(16Q11.2) MUTATED                                                    2
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 30(16Q11.2) MUTATED                                    1
  DEL PEAK 30(16Q11.2) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 30(16Q11.2) MUTATED                          1
  DEL PEAK 30(16Q11.2) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 30(16Q11.2) MUTATED                             3
  DEL PEAK 30(16Q11.2) WILD-TYPE                           1
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 30(16Q11.2) MUTATED                           1
  DEL PEAK 30(16Q11.2) WILD-TYPE                         0
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 30(16Q11.2) MUTATED                                   4
  DEL PEAK 30(16Q11.2) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 30(16Q11.2) MUTATED                                   4
  DEL PEAK 30(16Q11.2) WILD-TYPE                                 1
D55V3, multiclass
                                                         clus
vv                                                        DEL PEAK 30(16Q11.2) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            18
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                      29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  4
                                                         clus
vv                                                        DEL PEAK 30(16Q11.2) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                              10
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          1
  SUPERFICIAL TRUNK - FLANK                                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                                cls
clus                              0  1
  DEL PEAK 30(16Q11.2) MUTATED   77 53
  DEL PEAK 30(16Q11.2) WILD-TYPE 62 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q11.2) MUTATED     77   53
  DEL PEAK 30(16Q11.2) WILD-TYPE   62   65
        clus
vv       DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE
  FEMALE                           77                             62
  MALE                             53                             65
[1] 2 2
[1] FALSE
D55V5, binary
                                cls
clus                              0  1
  DEL PEAK 30(16Q11.2) MUTATED   84 42
  DEL PEAK 30(16Q11.2) WILD-TYPE 95 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q11.2) MUTATED     84   42
  DEL PEAK 30(16Q11.2) WILD-TYPE   95   30
     clus
vv    DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE
  NO                            84                             95
  YES                           42                             30
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 30(16Q11.2) MUTATED                             13             0
  DEL PEAK 30(16Q11.2) WILD-TYPE                           46             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 30(16Q11.2) MUTATED                                                                          0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 30(16Q11.2) MUTATED                     66
  DEL PEAK 30(16Q11.2) WILD-TYPE                   37
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 30(16Q11.2) MUTATED                                                  3
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 30(16Q11.2) MUTATED                 10
  DEL PEAK 30(16Q11.2) WILD-TYPE               14
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 30(16Q11.2) MUTATED                                                         20
  DEL PEAK 30(16Q11.2) WILD-TYPE                                                        8
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 30(16Q11.2) MUTATED                                          0
  DEL PEAK 30(16Q11.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 30(16Q11.2) MUTATED                             1
  DEL PEAK 30(16Q11.2) WILD-TYPE                           1
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 30(16Q11.2) MUTATED                               0
  DEL PEAK 30(16Q11.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 30(16Q11.2) MUTATED                                           17
  DEL PEAK 30(16Q11.2) WILD-TYPE                                          4
D55V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 30(16Q11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       13
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               66
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         17
                                                                          clus
vv                                                                         DEL PEAK 30(16Q11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         46
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 37
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 30(16Q11.2) MUTATED   73 41  4 11
  DEL PEAK 30(16Q11.2) WILD-TYPE 79 28  5 15
D55V7, multiclass
    clus
vv   DEL PEAK 30(16Q11.2) MUTATED DEL PEAK 30(16Q11.2) WILD-TYPE
  R0                           73                             79
  R1                           41                             28
  R2                            4                              5
  RX                           11                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q11.2) MUTATED       1                        14   109
  DEL PEAK 30(16Q11.2) WILD-TYPE     5                         4   115
D55V8, multiclass
                           clus
vv                          DEL PEAK 30(16Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              109
                           clus
vv                          DEL PEAK 30(16Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q11.2) MUTATED     3 111
  DEL PEAK 30(16Q11.2) WILD-TYPE   2 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q11.2) MUTATED      3  111
  DEL PEAK 30(16Q11.2) WILD-TYPE    2  109
                        clus
vv                       DEL PEAK 30(16Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       DEL PEAK 30(16Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            109
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 31(16Q23.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(16Q23.1) MUTATED   80 54
  DEL PEAK 31(16Q23.1) WILD-TYPE 79 44
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                           134                            123 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                            54                             44 
$`DEL PEAK 31(16Q23.1) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP 
       31.53        67.20        34.36        15.22        14.43        14.07 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 
       40.60        12.07        13.28       101.98        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       26.93        52.27        22.62        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
        6.35        18.08        20.94        17.52        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       50.01        19.69        88.57        25.25        10.32        38.47 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
       18.64        26.56        14.04        18.54        85.02        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 
        6.28         9.70        49.05        33.44        31.86        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K 
       14.99        10.68        68.55        50.43        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 
       24.26        52.77        46.03        26.47        59.84        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       82.68        36.33         3.06        16.87        86.30        64.21 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       62.20       152.12         9.34        38.17        40.77       150.35 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       40.44        36.69        60.66         6.58         1.15        12.00 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       66.74        77.88        50.40        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       19.89        15.48        67.63         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22        13.58        85.97         5.92        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU 
      101.26       123.78        23.38         5.19        63.81        35.28 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
       25.41        19.73        14.99        10.45         7.36        37.55 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01        13.08        17.65        46.82        48.59        35.90 
TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       37.12        16.77         8.61        19.63        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 
       12.46        84.79        38.27        65.46         8.58        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X9-A973 
       50.86        36.43 

$`DEL PEAK 31(16Q23.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-AB2H 
       36.30        34.68        16.18        75.32        17.95        15.85 
TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
      106.45        22.85        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-QQ-A8VB TCGA-WK-A8XT 
       16.60        52.11        28.21       159.29       188.15        41.49 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX 
       53.49        68.55        44.91        54.74        14.37        42.84 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03         0.56        32.71        68.61        12.85        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        95.38        79.17         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       86.83       136.44        44.68        35.77         4.54        73.87 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       34.88         9.73        35.28       108.82        37.58        37.41 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EQ 
       50.50       101.23        21.30        34.49        30.35        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS 
       48.20        20.05        61.97        45.14        47.87        27.95 
TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S 
       19.43        17.79        15.72        65.98        86.10         9.21 
TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3L4 
      106.55        50.89        71.31        49.15         8.05        34.88 
TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
       80.48       171.09         3.91        53.33        62.17        17.36 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
       16.41        30.31         0.49        21.73        17.98        22.39 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD 
       11.57       122.96        38.63         1.84        18.08       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      111.98        64.77        10.52         0.72        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       22.82        25.35        32.75        13.22        11.93         4.80 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB 
       22.62        63.35        45.34        29.46        27.32         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                        152.12                         188.15 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                         25.79                          34.68 
[1] "0.7 - 152.1 (25.8)" "0.5 - 188.2 (34.7)"
[1] "hr=" "1.3"
D56V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 31(16Q23.1) MUTATED                1                  3
  DEL PEAK 31(16Q23.1) WILD-TYPE              0                  4
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 31(16Q23.1) MUTATED                     0                   1
  DEL PEAK 31(16Q23.1) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 31(16Q23.1) MUTATED                               1
  DEL PEAK 31(16Q23.1) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 31(16Q23.1) MUTATED                       1                     19
  DEL PEAK 31(16Q23.1) WILD-TYPE                     0                      9
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 31(16Q23.1) MUTATED                      1                    0
  DEL PEAK 31(16Q23.1) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 31(16Q23.1) MUTATED                                       0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 31(16Q23.1) MUTATED                                  0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 31(16Q23.1) MUTATED                                                2
  DEL PEAK 31(16Q23.1) WILD-TYPE                                              0
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 31(16Q23.1) MUTATED                                 6
  DEL PEAK 31(16Q23.1) WILD-TYPE                               4
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 31(16Q23.1) MUTATED                                         0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 31(16Q23.1) MUTATED                              2
  DEL PEAK 31(16Q23.1) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 31(16Q23.1) MUTATED                         1
  DEL PEAK 31(16Q23.1) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 31(16Q23.1) MUTATED                                 14
  DEL PEAK 31(16Q23.1) WILD-TYPE                                3
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 31(16Q23.1) MUTATED                                         3
  DEL PEAK 31(16Q23.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 31(16Q23.1) MUTATED                             25
  DEL PEAK 31(16Q23.1) WILD-TYPE                           19
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 31(16Q23.1) MUTATED                                         0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 31(16Q23.1) MUTATED                                           1
  DEL PEAK 31(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 31(16Q23.1) MUTATED                                                  2
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 31(16Q23.1) MUTATED                                          5
  DEL PEAK 31(16Q23.1) WILD-TYPE                                        3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 31(16Q23.1) MUTATED                                                         0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 31(16Q23.1) MUTATED                                            0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                          1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 31(16Q23.1) MUTATED                                                  29
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                44
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 31(16Q23.1) MUTATED                                                    2
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 31(16Q23.1) MUTATED                                    2
  DEL PEAK 31(16Q23.1) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 31(16Q23.1) MUTATED                          1
  DEL PEAK 31(16Q23.1) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 31(16Q23.1) MUTATED                             3
  DEL PEAK 31(16Q23.1) WILD-TYPE                           1
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 31(16Q23.1) MUTATED                           1
  DEL PEAK 31(16Q23.1) WILD-TYPE                         0
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 31(16Q23.1) MUTATED                                   4
  DEL PEAK 31(16Q23.1) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 31(16Q23.1) MUTATED                                   4
  DEL PEAK 31(16Q23.1) WILD-TYPE                                 1
D56V3, multiclass
                                                         clus
vv                                                        DEL PEAK 31(16Q23.1) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            19
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                  14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 29
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        3
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  4
                                                         clus
vv                                                        DEL PEAK 31(16Q23.1) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   4
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                0
  GYNECOLOGICAL - UTERUS                                                               9
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                     3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   44
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          1
  SUPERFICIAL TRUNK - FLANK                                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                                cls
clus                              0  1
  DEL PEAK 31(16Q23.1) MUTATED   79 55
  DEL PEAK 31(16Q23.1) WILD-TYPE 60 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED     79   55
  DEL PEAK 31(16Q23.1) WILD-TYPE   60   63
        clus
vv       DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  FEMALE                           79                             60
  MALE                             55                             63
[1] 2 2
[1] FALSE
D56V5, binary
                                cls
clus                              0  1
  DEL PEAK 31(16Q23.1) MUTATED   90 41
  DEL PEAK 31(16Q23.1) WILD-TYPE 89 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED     90   41
  DEL PEAK 31(16Q23.1) WILD-TYPE   89   31
     clus
vv    DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  NO                            90                             89
  YES                           41                             31
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 31(16Q23.1) MUTATED                             14             0
  DEL PEAK 31(16Q23.1) WILD-TYPE                           45             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 31(16Q23.1) MUTATED                                                                          0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 31(16Q23.1) MUTATED                     68
  DEL PEAK 31(16Q23.1) WILD-TYPE                   35
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 31(16Q23.1) MUTATED                                                  2
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                7
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 31(16Q23.1) MUTATED                 13
  DEL PEAK 31(16Q23.1) WILD-TYPE               11
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 31(16Q23.1) MUTATED                                                         18
  DEL PEAK 31(16Q23.1) WILD-TYPE                                                       10
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 31(16Q23.1) MUTATED                                          0
  DEL PEAK 31(16Q23.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 31(16Q23.1) MUTATED                             1
  DEL PEAK 31(16Q23.1) WILD-TYPE                           1
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 31(16Q23.1) MUTATED                               0
  DEL PEAK 31(16Q23.1) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 31(16Q23.1) MUTATED                                           18
  DEL PEAK 31(16Q23.1) WILD-TYPE                                          3
D56V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 31(16Q23.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       14
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               68
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    2
  MYXOFIBROSARCOMA                                                                                   13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         18
                                                                          clus
vv                                                                         DEL PEAK 31(16Q23.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         45
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 35
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      7
  MYXOFIBROSARCOMA                                                                                     11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 31(16Q23.1) MUTATED   74 44  4 11
  DEL PEAK 31(16Q23.1) WILD-TYPE 78 25  5 15
D56V7, multiclass
    clus
vv   DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  R0                           74                             78
  R1                           44                             25
  R2                            4                              5
  RX                           11                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(16Q23.1) MUTATED       4                        13   112
  DEL PEAK 31(16Q23.1) WILD-TYPE     2                         5   112
D56V8, multiclass
                           clus
vv                          DEL PEAK 31(16Q23.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              112
                           clus
vv                          DEL PEAK 31(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q23.1) MUTATED     2 118
  DEL PEAK 31(16Q23.1) WILD-TYPE   3 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED      2  118
  DEL PEAK 31(16Q23.1) WILD-TYPE    3  102
                        clus
vv                       DEL PEAK 31(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       DEL PEAK 31(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 32(17P13.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(17P13.1) MUTATED   88 41
  DEL PEAK 32(17P13.1) WILD-TYPE 71 57
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                           129                            128 
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                            41                             57 
$`DEL PEAK 32(17P13.1) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG 
       31.53        16.18        67.20        75.32        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HB-A5W3 
       14.43        14.07        12.07       101.98        30.51        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-KF-A41W TCGA-PC-A5DP 
       52.11        26.93        52.27        28.21        11.70        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HL 
       20.94       188.15        17.52        26.17        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A23R 
       38.47        36.03        18.64        26.56        45.11        74.66 
TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UE TCGA-DX-A48J 
       49.05        51.02        14.99        10.68        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        24.26        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS 
       59.84        37.58        37.41        82.68        36.33        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       50.50        16.87        86.30       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR 
       62.20       152.12         9.34        47.87        40.77       150.35 
TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q 
       40.44         6.58         1.15        17.79        86.10        66.74 
TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-HB-A2OT 
       77.88        50.40        31.13        20.32        15.48        67.63 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72         9.80        80.48         3.22         1.38 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       19.89       171.09         5.92        16.41         3.91       101.26 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
       62.17        23.38         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QC-AA9N 
       25.41         0.49        21.73       122.96        37.55        17.65 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       35.90        37.12        10.52        16.77         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75         8.61        19.63        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93        84.79        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       63.35        26.43        18.08        30.84        19.17        20.65 
TCGA-X6-A8C5 TCGA-X9-A971 TCGA-Z4-AAPG 
       50.86        27.32        15.98 

$`DEL PEAK 32(17P13.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       36.30        34.68        34.36        15.85        40.60       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       13.28        22.85        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       37.02       159.29        22.62        17.75         8.28         6.35 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3R-A8YX 
       41.49        35.08        44.91        54.74        14.37         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        32.71        68.61        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       31.86        35.77         4.54        73.87        68.55        50.43 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       85.45        35.28        15.95        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6Z0 TCGA-DX-A7EN TCGA-DX-A7EQ 
       26.99         3.06        41.00        64.21        30.35        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BS 
       48.20        20.05        61.97        45.14        38.17        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       36.69        60.66        19.43        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE 
        9.21       106.55        50.89        71.31        49.15        21.70 
TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-IE-A4EI TCGA-IF-A3RQ 
       19.89         8.05        34.88         4.57        19.53        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42X 
       25.22        13.58        85.97         1.05        53.33       123.78 
TCGA-K1-A6RT TCGA-KD-A5QU TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       17.36        35.28        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       11.57        10.45         7.36        38.63        81.01        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
        1.84        46.82        18.08        48.59       130.32       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WP-A9GB 
       64.77         0.72        18.94        13.22         4.80         8.58 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       35.90        45.34        35.18        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                          0.49                           0.56 
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE 
                        28.210                         33.075 
[1] "0.5 - 188.2 (28.2)" "0.6 - 159.3 (33.1)"
[1] "hr=" "1.4"
D57V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 32(17P13.1) MUTATED                0                  4
  DEL PEAK 32(17P13.1) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 32(17P13.1) MUTATED                     0                   1
  DEL PEAK 32(17P13.1) WILD-TYPE                   2                   0
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 32(17P13.1) MUTATED                               1
  DEL PEAK 32(17P13.1) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 32(17P13.1) MUTATED                       0                     16
  DEL PEAK 32(17P13.1) WILD-TYPE                     1                     12
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 32(17P13.1) MUTATED                      0                    0
  DEL PEAK 32(17P13.1) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 32(17P13.1) MUTATED                                       0
  DEL PEAK 32(17P13.1) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 32(17P13.1) MUTATED                                  0
  DEL PEAK 32(17P13.1) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 32(17P13.1) MUTATED                                                1
  DEL PEAK 32(17P13.1) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 32(17P13.1) MUTATED                                 3
  DEL PEAK 32(17P13.1) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 32(17P13.1) MUTATED                                         0
  DEL PEAK 32(17P13.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 32(17P13.1) MUTATED                              2
  DEL PEAK 32(17P13.1) WILD-TYPE                            2
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 32(17P13.1) MUTATED                         0
  DEL PEAK 32(17P13.1) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 32(17P13.1) MUTATED                                 10
  DEL PEAK 32(17P13.1) WILD-TYPE                                7
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 32(17P13.1) MUTATED                                         3
  DEL PEAK 32(17P13.1) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 32(17P13.1) MUTATED                             27
  DEL PEAK 32(17P13.1) WILD-TYPE                           17
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 32(17P13.1) MUTATED                                         4
  DEL PEAK 32(17P13.1) WILD-TYPE                                       0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 32(17P13.1) MUTATED                                           1
  DEL PEAK 32(17P13.1) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 32(17P13.1) MUTATED                                                  1
  DEL PEAK 32(17P13.1) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 32(17P13.1) MUTATED                                          4
  DEL PEAK 32(17P13.1) WILD-TYPE                                        4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 32(17P13.1) MUTATED                                                         1
  DEL PEAK 32(17P13.1) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 32(17P13.1) MUTATED                                            1
  DEL PEAK 32(17P13.1) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 32(17P13.1) MUTATED                                                  28
  DEL PEAK 32(17P13.1) WILD-TYPE                                                45
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 32(17P13.1) MUTATED                                                    2
  DEL PEAK 32(17P13.1) WILD-TYPE                                                  1
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 32(17P13.1) MUTATED                                    2
  DEL PEAK 32(17P13.1) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 32(17P13.1) MUTATED                          2
  DEL PEAK 32(17P13.1) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 32(17P13.1) MUTATED                             4
  DEL PEAK 32(17P13.1) WILD-TYPE                           0
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 32(17P13.1) MUTATED                           1
  DEL PEAK 32(17P13.1) WILD-TYPE                         0
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 32(17P13.1) MUTATED                                   5
  DEL PEAK 32(17P13.1) WILD-TYPE                                 2
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 32(17P13.1) MUTATED                                   4
  DEL PEAK 32(17P13.1) WILD-TYPE                                 1
D57V3, multiclass
                                                         clus
vv                                                        DEL PEAK 32(17P13.1) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                            16
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       2
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  4
                                                         clus
vv                                                        DEL PEAK 32(17P13.1) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              12
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         2
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          0
  SUPERFICIAL TRUNK - FLANK                                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                                cls
clus                              0  1
  DEL PEAK 32(17P13.1) MUTATED   78 51
  DEL PEAK 32(17P13.1) WILD-TYPE 61 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.1) MUTATED     78   51
  DEL PEAK 32(17P13.1) WILD-TYPE   61   67
        clus
vv       DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE
  FEMALE                           78                             61
  MALE                             51                             67
[1] 2 2
[1] FALSE
D57V5, binary
                                cls
clus                              0  1
  DEL PEAK 32(17P13.1) MUTATED   81 43
  DEL PEAK 32(17P13.1) WILD-TYPE 98 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.1) MUTATED     81   43
  DEL PEAK 32(17P13.1) WILD-TYPE   98   29
     clus
vv    DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE
  NO                            81                             98
  YES                           43                             29
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 32(17P13.1) MUTATED                             11             0
  DEL PEAK 32(17P13.1) WILD-TYPE                           48             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 32(17P13.1) MUTATED                                                                          0
  DEL PEAK 32(17P13.1) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 32(17P13.1) MUTATED                     66
  DEL PEAK 32(17P13.1) WILD-TYPE                   37
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 32(17P13.1) MUTATED                                                  7
  DEL PEAK 32(17P13.1) WILD-TYPE                                                2
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 32(17P13.1) MUTATED                 13
  DEL PEAK 32(17P13.1) WILD-TYPE               11
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 32(17P13.1) MUTATED                                                         16
  DEL PEAK 32(17P13.1) WILD-TYPE                                                       12
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 32(17P13.1) MUTATED                                          0
  DEL PEAK 32(17P13.1) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 32(17P13.1) MUTATED                             1
  DEL PEAK 32(17P13.1) WILD-TYPE                           1
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 32(17P13.1) MUTATED                               0
  DEL PEAK 32(17P13.1) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 32(17P13.1) MUTATED                                           15
  DEL PEAK 32(17P13.1) WILD-TYPE                                          6
D57V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 32(17P13.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       11
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               66
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    7
  MYXOFIBROSARCOMA                                                                                   13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         15
                                                                          clus
vv                                                                         DEL PEAK 32(17P13.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         48
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 37
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      2
  MYXOFIBROSARCOMA                                                                                     11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           1
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 32(17P13.1) MUTATED   81 31  3 13
  DEL PEAK 32(17P13.1) WILD-TYPE 71 38  6 13
D57V7, multiclass
    clus
vv   DEL PEAK 32(17P13.1) MUTATED DEL PEAK 32(17P13.1) WILD-TYPE
  R0                           81                             71
  R1                           31                             38
  R2                            3                              6
  RX                           13                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(17P13.1) MUTATED       2                        13   108
  DEL PEAK 32(17P13.1) WILD-TYPE     4                         5   116
D57V8, multiclass
                           clus
vv                          DEL PEAK 32(17P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              108
                           clus
vv                          DEL PEAK 32(17P13.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(17P13.1) MUTATED     3 109
  DEL PEAK 32(17P13.1) WILD-TYPE   2 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17P13.1) MUTATED      3  109
  DEL PEAK 32(17P13.1) WILD-TYPE    2  111
                        clus
vv                       DEL PEAK 32(17P13.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       DEL PEAK 32(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            111
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 33(17Q11.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(17Q11.2) MUTATED    48  33
  DEL PEAK 33(17Q11.2) WILD-TYPE 111  65
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                            81                            176 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                            33                             65 
$`DEL PEAK 33(17Q11.2) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       31.53        34.68        67.20        34.36        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 
       14.43        14.07       106.45        13.28       101.98        30.51 
TCGA-DX-AB3A TCGA-HB-A43Z TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB 
       32.15        37.02        17.75         6.35        20.94       188.15 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-3R-A8YX 
       35.08        50.01        19.69        42.84        26.56         0.56 
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW 
       45.11        74.66         6.28         9.70        49.05       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L 
       44.68        14.99        10.68        50.43        85.45        24.26 
TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       15.95        31.96         3.06        41.00        78.28        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BK 
       16.87        86.30        21.30        34.49         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2T 
       45.14        36.69         6.58        17.79        86.10        77.88 
TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A75J 
       67.63         3.22        19.89        25.22         5.92         3.91 
TCGA-K1-A42W TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-N1-A6IA 
       62.17         5.19        25.41        21.73        19.73         7.36 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       17.65        46.82        35.90        18.94         3.88        22.82 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX TCGA-WK-A8Y0 
       32.75        19.63        13.41        10.72        38.27        22.62 
TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-Z4-AAPG 
       45.34        20.65        15.98 

$`DEL PEAK 33(17Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       36.30        16.18        75.32        15.85        40.60        12.07 
TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 
       22.85        60.00        84.66        16.60        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP 
        8.28        18.08        17.52        26.17        41.49        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1KW 
       10.32        38.47        36.03        18.64        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       68.61        12.85        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LY 
        8.58        95.38        79.17         9.04        86.83        33.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       31.86        35.77        51.02         4.54        73.87        68.55 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        45.99        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       36.33        28.96        36.85        26.99        64.21       101.23 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       47.87        38.17        40.77       150.35        27.95        40.44 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43         1.15        12.00        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       66.74         9.21       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       49.15        31.13        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA 
       80.48        19.53         1.38        37.12       171.09        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       85.97        16.41         1.05       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       17.36        23.38        63.81        16.41        35.28        30.31 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        0.49        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 
      122.96        37.55        38.63        81.01        13.08         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT 
       10.52         0.72        16.77        25.35         8.61        13.22 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WP-A9GB 
       12.46        11.93         4.80        84.79        65.46         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                          0.56                           0.49 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                        188.15                         171.09 
  DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE 
                         25.22                          33.37 
[1] "0.6 - 188.2 (25.2)" "0.5 - 171.1 (33.4)"
[1] "hr=" "1.3"
D58V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 33(17Q11.2) MUTATED                1                  6
  DEL PEAK 33(17Q11.2) WILD-TYPE              0                  1
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 33(17Q11.2) MUTATED                     0                   0
  DEL PEAK 33(17Q11.2) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 33(17Q11.2) MUTATED                               0
  DEL PEAK 33(17Q11.2) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 33(17Q11.2) MUTATED                       0                      4
  DEL PEAK 33(17Q11.2) WILD-TYPE                     1                     24
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 33(17Q11.2) MUTATED                      0                    0
  DEL PEAK 33(17Q11.2) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 33(17Q11.2) MUTATED                                       0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 33(17Q11.2) MUTATED                                  0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 33(17Q11.2) MUTATED                                                1
  DEL PEAK 33(17Q11.2) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 33(17Q11.2) MUTATED                                 0
  DEL PEAK 33(17Q11.2) WILD-TYPE                              10
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 33(17Q11.2) MUTATED                                         0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 33(17Q11.2) MUTATED                              1
  DEL PEAK 33(17Q11.2) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 33(17Q11.2) MUTATED                         0
  DEL PEAK 33(17Q11.2) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 33(17Q11.2) MUTATED                                  7
  DEL PEAK 33(17Q11.2) WILD-TYPE                               10
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 33(17Q11.2) MUTATED                                         5
  DEL PEAK 33(17Q11.2) WILD-TYPE                                       0
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 33(17Q11.2) MUTATED                             20
  DEL PEAK 33(17Q11.2) WILD-TYPE                           24
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 33(17Q11.2) MUTATED                                         1
  DEL PEAK 33(17Q11.2) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 33(17Q11.2) MUTATED                                           0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 33(17Q11.2) MUTATED                                                  1
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 33(17Q11.2) MUTATED                                          2
  DEL PEAK 33(17Q11.2) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 33(17Q11.2) MUTATED                                                         0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 33(17Q11.2) MUTATED                                            1
  DEL PEAK 33(17Q11.2) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 33(17Q11.2) MUTATED                                                  18
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                55
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 33(17Q11.2) MUTATED                                                    0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 33(17Q11.2) MUTATED                                    2
  DEL PEAK 33(17Q11.2) WILD-TYPE                                  0
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 33(17Q11.2) MUTATED                          1
  DEL PEAK 33(17Q11.2) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 33(17Q11.2) MUTATED                             4
  DEL PEAK 33(17Q11.2) WILD-TYPE                           0
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 33(17Q11.2) MUTATED                           0
  DEL PEAK 33(17Q11.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 33(17Q11.2) MUTATED                                   4
  DEL PEAK 33(17Q11.2) WILD-TYPE                                 3
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 33(17Q11.2) MUTATED                                   2
  DEL PEAK 33(17Q11.2) WILD-TYPE                                 3
D58V3, multiclass
                                                         clus
vv                                                        DEL PEAK 33(17Q11.2) MUTATED
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 6
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             4
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            5
  LOWER EXTREMITY - THIGH/KNEE                                                      20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 2
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        4
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK 33(17Q11.2) WILD-TYPE
  CHEST - BREAST                                                                       0
  CHEST - CHEST WALL                                                                   1
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              24
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              0
  LOWER EXTREMITY - THIGH/KNEE                                                        24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   55
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   0
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          0
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                cls
clus                              0  1
  DEL PEAK 33(17Q11.2) MUTATED   40 41
  DEL PEAK 33(17Q11.2) WILD-TYPE 99 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(17Q11.2) MUTATED     40   41
  DEL PEAK 33(17Q11.2) WILD-TYPE   99   77
        clus
vv       DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  FEMALE                           40                             99
  MALE                             41                             77
[1] 2 2
[1] FALSE
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 33(17Q11.2) MUTATED    48  32
  DEL PEAK 33(17Q11.2) WILD-TYPE 131  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(17Q11.2) MUTATED     48   32
  DEL PEAK 33(17Q11.2) WILD-TYPE  131   40
     clus
vv    DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  NO                            48                            131
  YES                           32                             40
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 33(17Q11.2) MUTATED                             17             0
  DEL PEAK 33(17Q11.2) WILD-TYPE                           42             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 33(17Q11.2) MUTATED                                                                          0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 33(17Q11.2) MUTATED                     21
  DEL PEAK 33(17Q11.2) WILD-TYPE                   82
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 33(17Q11.2) MUTATED                                                  4
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                5
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 33(17Q11.2) MUTATED                 13
  DEL PEAK 33(17Q11.2) WILD-TYPE               11
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 33(17Q11.2) MUTATED                                                         15
  DEL PEAK 33(17Q11.2) WILD-TYPE                                                       13
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 33(17Q11.2) MUTATED                                          0
  DEL PEAK 33(17Q11.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 33(17Q11.2) MUTATED                             0
  DEL PEAK 33(17Q11.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 33(17Q11.2) MUTATED                               0
  DEL PEAK 33(17Q11.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 33(17Q11.2) MUTATED                                           11
  DEL PEAK 33(17Q11.2) WILD-TYPE                                         10
D58V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 33(17Q11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       17
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    4
  MYXOFIBROSARCOMA                                                                                   13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         11
                                                                          clus
vv                                                                         DEL PEAK 33(17Q11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         42
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      5
  MYXOFIBROSARCOMA                                                                                     11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           10
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(17Q11.2) MUTATED    48  23   4   6
  DEL PEAK 33(17Q11.2) WILD-TYPE 104  46   5  20
D58V7, multiclass
    clus
vv   DEL PEAK 33(17Q11.2) MUTATED DEL PEAK 33(17Q11.2) WILD-TYPE
  R0                           48                            104
  R1                           23                             46
  R2                            4                              5
  RX                            6                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(17Q11.2) MUTATED       1                         7    70
  DEL PEAK 33(17Q11.2) WILD-TYPE     5                        11   154
D58V8, multiclass
                           clus
vv                          DEL PEAK 33(17Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               70
                           clus
vv                          DEL PEAK 33(17Q11.2) WILD-TYPE
  ASIAN                                                  5
  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"
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(17Q11.2) MUTATED     1  70
  DEL PEAK 33(17Q11.2) WILD-TYPE   4 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(17Q11.2) MUTATED      1   70
  DEL PEAK 33(17Q11.2) WILD-TYPE    4  150
                        clus
vv                       DEL PEAK 33(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       DEL PEAK 33(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            150
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 34(17Q25.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(17Q25.3) MUTATED    37  30
  DEL PEAK 34(17Q25.3) WILD-TYPE 122  68
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                            67                            190 
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                            30                             68 
$`DEL PEAK 34(17Q25.3) MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2W 
       31.53        34.68        15.22        14.07        15.85       106.45 
TCGA-DX-AB35 TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM 
       30.51        12.62        26.93        11.70        17.75         6.35 
TCGA-3B-A9HI TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX 
       50.01        68.55        88.57        26.56        32.71        68.61 
TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 
       18.54        74.66         6.28        49.05        33.44        44.68 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 
       14.99        50.43        34.88        85.45        24.26        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BK 
       82.68        36.33         3.06        34.49         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2T 
       45.14        36.69         6.58         1.15        86.10        77.88 
TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-JV-A5VE 
       31.13        33.30         3.22        25.22        13.58        16.41 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       62.17       123.78         5.19        63.81        16.41        35.28 
TCGA-MB-A8JK TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VH 
       21.73        37.55        17.65        46.82        48.59        10.52 
TCGA-SI-A71O TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.82        38.27         8.58        45.34        19.17        20.65 
TCGA-Z4-AAPG 
       15.98 

$`DEL PEAK 34(17Q25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        16.18        67.20        34.36        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       14.43        40.60        12.07        13.28        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 
       60.00        84.66        32.15        16.60        37.02        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DP 
       52.27        28.21       159.29        22.62         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       19.69        53.49        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       42.84        10.32        38.47        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        45.11        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        95.38        79.17         9.04        86.83 
TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
      136.44        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       73.87        68.55         9.73        45.99        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       50.50        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       47.87        38.17        40.77       150.35        27.95        40.44 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43        17.79        12.00        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       66.74         9.21       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       67.63        34.88         4.57         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 
       19.53         1.38        19.89        37.12       171.09        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT 
        5.92         1.05         3.91       101.26        53.33        17.36 
TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       23.38        30.31        25.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        81.01        13.08         1.84        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        64.77         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         3.88        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       84.79        65.46        22.62        63.35        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       18.08        30.84        35.18        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                          1.15                           0.49 
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                        123.78                         188.15 
  DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE 
                         31.13                          31.35 
[1] "1.1 - 123.8 (31.1)" "0.5 - 188.2 (31.4)"
[1] "hr=" "1.4"
D59V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 34(17Q25.3) MUTATED                0                  1
  DEL PEAK 34(17Q25.3) WILD-TYPE              1                  6
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 34(17Q25.3) MUTATED                     0                   0
  DEL PEAK 34(17Q25.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 34(17Q25.3) MUTATED                               1
  DEL PEAK 34(17Q25.3) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 34(17Q25.3) MUTATED                       0                      8
  DEL PEAK 34(17Q25.3) WILD-TYPE                     1                     20
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 34(17Q25.3) MUTATED                      0                    0
  DEL PEAK 34(17Q25.3) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 34(17Q25.3) MUTATED                                       0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 34(17Q25.3) MUTATED                                  0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 34(17Q25.3) MUTATED                                                1
  DEL PEAK 34(17Q25.3) WILD-TYPE                                              1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 34(17Q25.3) MUTATED                                 4
  DEL PEAK 34(17Q25.3) WILD-TYPE                               6
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 34(17Q25.3) MUTATED                                         0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 34(17Q25.3) MUTATED                              0
  DEL PEAK 34(17Q25.3) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 34(17Q25.3) MUTATED                         1
  DEL PEAK 34(17Q25.3) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 34(17Q25.3) MUTATED                                  6
  DEL PEAK 34(17Q25.3) WILD-TYPE                               11
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 34(17Q25.3) MUTATED                                         3
  DEL PEAK 34(17Q25.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 34(17Q25.3) MUTATED                             10
  DEL PEAK 34(17Q25.3) WILD-TYPE                           34
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 34(17Q25.3) MUTATED                                         0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 34(17Q25.3) MUTATED                                           0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 34(17Q25.3) MUTATED                                                  1
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 34(17Q25.3) MUTATED                                          3
  DEL PEAK 34(17Q25.3) WILD-TYPE                                        5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 34(17Q25.3) MUTATED                                                         0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 34(17Q25.3) MUTATED                                            1
  DEL PEAK 34(17Q25.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 34(17Q25.3) MUTATED                                                  19
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                54
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 34(17Q25.3) MUTATED                                                    0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 34(17Q25.3) MUTATED                                    1
  DEL PEAK 34(17Q25.3) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 34(17Q25.3) MUTATED                          1
  DEL PEAK 34(17Q25.3) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 34(17Q25.3) MUTATED                             2
  DEL PEAK 34(17Q25.3) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 34(17Q25.3) MUTATED                           0
  DEL PEAK 34(17Q25.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 34(17Q25.3) MUTATED                                   2
  DEL PEAK 34(17Q25.3) WILD-TYPE                                 5
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 34(17Q25.3) MUTATED                                   2
  DEL PEAK 34(17Q25.3) WILD-TYPE                                 3
D59V3, multiclass
                                                         clus
vv                                                        DEL PEAK 34(17Q25.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 1
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             8
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 19
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  2
                                                         clus
vv                                                        DEL PEAK 34(17Q25.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   6
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              20
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   54
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(17Q25.3) MUTATED    36  31
  DEL PEAK 34(17Q25.3) WILD-TYPE 103  87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(17Q25.3) MUTATED     36   31
  DEL PEAK 34(17Q25.3) WILD-TYPE  103   87
        clus
vv       DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE
  FEMALE                           36                            103
  MALE                             31                             87
[1] 2 2
[1] FALSE
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 34(17Q25.3) MUTATED    44  20
  DEL PEAK 34(17Q25.3) WILD-TYPE 135  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(17Q25.3) MUTATED     44   20
  DEL PEAK 34(17Q25.3) WILD-TYPE  135   52
     clus
vv    DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE
  NO                            44                            135
  YES                           20                             52
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 34(17Q25.3) MUTATED                             14             0
  DEL PEAK 34(17Q25.3) WILD-TYPE                           45             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 34(17Q25.3) MUTATED                                                                          0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 34(17Q25.3) MUTATED                     32
  DEL PEAK 34(17Q25.3) WILD-TYPE                   71
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 34(17Q25.3) MUTATED                                                  2
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                7
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 34(17Q25.3) MUTATED                  3
  DEL PEAK 34(17Q25.3) WILD-TYPE               21
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 34(17Q25.3) MUTATED                                                         11
  DEL PEAK 34(17Q25.3) WILD-TYPE                                                       17
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 34(17Q25.3) MUTATED                                          0
  DEL PEAK 34(17Q25.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 34(17Q25.3) MUTATED                             0
  DEL PEAK 34(17Q25.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 34(17Q25.3) MUTATED                               0
  DEL PEAK 34(17Q25.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 34(17Q25.3) MUTATED                                            5
  DEL PEAK 34(17Q25.3) WILD-TYPE                                         16
D59V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 34(17Q25.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       14
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    2
  MYXOFIBROSARCOMA                                                                                    3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          5
                                                                          clus
vv                                                                         DEL PEAK 34(17Q25.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         45
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      7
  MYXOFIBROSARCOMA                                                                                     21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(17Q25.3) MUTATED    36  21   2   8
  DEL PEAK 34(17Q25.3) WILD-TYPE 116  48   7  18
D59V7, multiclass
    clus
vv   DEL PEAK 34(17Q25.3) MUTATED DEL PEAK 34(17Q25.3) WILD-TYPE
  R0                           36                            116
  R1                           21                             48
  R2                            2                              7
  RX                            8                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(17Q25.3) MUTATED       1                         6    57
  DEL PEAK 34(17Q25.3) WILD-TYPE     5                        12   167
D59V8, multiclass
                           clus
vv                          DEL PEAK 34(17Q25.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               57
                           clus
vv                          DEL PEAK 34(17Q25.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(17Q25.3) MUTATED     0  60
  DEL PEAK 34(17Q25.3) WILD-TYPE   5 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(17Q25.3) MUTATED      0   60
  DEL PEAK 34(17Q25.3) WILD-TYPE    5  160
                        clus
vv                       DEL PEAK 34(17Q25.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 34(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            160
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 35(18P11.32) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(18P11.32) MUTATED    40  28
  DEL PEAK 35(18P11.32) WILD-TYPE 119  70
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                             68                             189 
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                             28                              70 
$`DEL PEAK 35(18P11.32) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB32 
       31.53        67.20        15.22        17.95        14.43       101.98 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A6FX 
       37.02        12.62        26.93        11.70        18.08        20.94 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3R-A8YX 
       35.08        50.01        19.69        25.25        42.84         0.56 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3M1 
       68.61        12.85        18.54         9.70        49.05        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF 
       31.86        51.02        14.99        10.68        68.55        85.45 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BJ 
       46.03        26.47        31.96        34.49        62.20         9.34 
TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-FX-A3TO 
       40.44         6.58        17.79        12.00        15.72        20.32 
TCGA-HB-A2OT TCGA-IE-A4EI TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF 
       67.63        19.53       171.09        85.97         5.92         1.05 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QC-AA9N 
       16.41        35.28        25.41        37.55        13.08        17.65 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G 
       10.52         3.88        25.35         8.61        19.63        10.72 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A7WD 
       84.79        38.27        65.46        22.62        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C4 
       35.18        20.65 

$`DEL PEAK 35(18P11.32) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BP 
       36.30        34.68        16.18        34.36        75.32        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       15.85        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 
       30.51        60.00        84.66        32.15        16.60        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.27        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP 
        6.35       188.15        17.52        26.17        41.49        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HY 
       68.55        88.57        44.91        54.74        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW 
       38.47        36.03        18.64        26.56        14.04        32.71 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        95.38        79.17         9.04        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       33.44        35.77         4.54        73.87        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U 
        9.73        45.99        24.26        35.28        52.77       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        36.85        26.99         3.06        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       50.50        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2L TCGA-DX-AB2O 
       36.69        60.66        19.43         1.15        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       71.31        49.15        31.13        21.70        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48         3.22         1.38        19.89        37.12        25.22 
TCGA-IS-A3KA TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       13.58        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-LI-A67I 
      123.78        17.36        23.38         5.19        63.81        30.31 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       11.57        10.45         7.36       122.96        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32       111.98        64.77         0.72        16.77        18.94 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO 
       22.82        32.75        13.22        13.41        12.46        11.93 
TCGA-WK-A8XQ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
        4.80         8.58        63.35        26.43        35.90        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                           0.56                            0.49 
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                         171.09                          188.15 
  DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE 
                         23.935                          33.530 
[1] "0.6 - 171.1 (23.9)" "0.5 - 188.2 (33.5)"
[1] "hr=" "1.4"
D60V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 35(18P11.32) MUTATED                0                  3
  DEL PEAK 35(18P11.32) WILD-TYPE              1                  4
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 35(18P11.32) MUTATED                     0                   0
  DEL PEAK 35(18P11.32) WILD-TYPE                   2                   1
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 35(18P11.32) MUTATED                               1
  DEL PEAK 35(18P11.32) WILD-TYPE                             1
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 35(18P11.32) MUTATED                       0                      9
  DEL PEAK 35(18P11.32) WILD-TYPE                     1                     19
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 35(18P11.32) MUTATED                      1                    0
  DEL PEAK 35(18P11.32) WILD-TYPE                    1                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 35(18P11.32) MUTATED                                       0
  DEL PEAK 35(18P11.32) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 35(18P11.32) MUTATED                                  0
  DEL PEAK 35(18P11.32) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 35(18P11.32) MUTATED                                                1
  DEL PEAK 35(18P11.32) WILD-TYPE                                              1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 35(18P11.32) MUTATED                                 2
  DEL PEAK 35(18P11.32) WILD-TYPE                               8
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 35(18P11.32) MUTATED                                         0
  DEL PEAK 35(18P11.32) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 35(18P11.32) MUTATED                              1
  DEL PEAK 35(18P11.32) WILD-TYPE                            3
                                 vv
clus                              LOWER EXTREMITY - GROIN
  DEL PEAK 35(18P11.32) MUTATED                         0
  DEL PEAK 35(18P11.32) WILD-TYPE                       2
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 35(18P11.32) MUTATED                                  4
  DEL PEAK 35(18P11.32) WILD-TYPE                               13
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 35(18P11.32) MUTATED                                         1
  DEL PEAK 35(18P11.32) WILD-TYPE                                       4
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 35(18P11.32) MUTATED                              8
  DEL PEAK 35(18P11.32) WILD-TYPE                           36
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 35(18P11.32) MUTATED                                         1
  DEL PEAK 35(18P11.32) WILD-TYPE                                       3
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 35(18P11.32) MUTATED                                           1
  DEL PEAK 35(18P11.32) WILD-TYPE                                         1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 35(18P11.32) MUTATED                                                  1
  DEL PEAK 35(18P11.32) WILD-TYPE                                                4
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 35(18P11.32) MUTATED                                          2
  DEL PEAK 35(18P11.32) WILD-TYPE                                        6
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 35(18P11.32) MUTATED                                                         0
  DEL PEAK 35(18P11.32) WILD-TYPE                                                       2
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 35(18P11.32) MUTATED                                            0
  DEL PEAK 35(18P11.32) WILD-TYPE                                          1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 35(18P11.32) MUTATED                                                  21
  DEL PEAK 35(18P11.32) WILD-TYPE                                                52
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 35(18P11.32) MUTATED                                                    1
  DEL PEAK 35(18P11.32) WILD-TYPE                                                  2
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 35(18P11.32) MUTATED                                    2
  DEL PEAK 35(18P11.32) WILD-TYPE                                  0
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  DEL PEAK 35(18P11.32) MUTATED                          1
  DEL PEAK 35(18P11.32) WILD-TYPE                        4
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 35(18P11.32) MUTATED                             2
  DEL PEAK 35(18P11.32) WILD-TYPE                           2
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  DEL PEAK 35(18P11.32) MUTATED                           0
  DEL PEAK 35(18P11.32) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 35(18P11.32) MUTATED                                   2
  DEL PEAK 35(18P11.32) WILD-TYPE                                 5
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 35(18P11.32) MUTATED                                   2
  DEL PEAK 35(18P11.32) WILD-TYPE                                 3
D60V3, multiclass
                                                         clus
vv                                                        DEL PEAK 35(18P11.32) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                              9
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        1
  LOWER EXTREMITY - GROIN                                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                                    4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                        8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            1
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
                                                         clus
vv                                                        DEL PEAK 35(18P11.32) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    4
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                                         1
  GYNECOLOGICAL - OVARY                                                                 1
  GYNECOLOGICAL - UTERUS                                                               19
  HEAD AND NECK - HEAD                                                                  1
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          3
  LOWER EXTREMITY - GROIN                                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               4
  LOWER EXTREMITY - THIGH/KNEE                                                         36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    52
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    0
  SUPERFICIAL TRUNK - BACK                                                              4
  SUPERFICIAL TRUNK - BUTTOCK                                                           2
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                                 cls
clus                                0   1
  DEL PEAK 35(18P11.32) MUTATED    39  29
  DEL PEAK 35(18P11.32) WILD-TYPE 100  89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(18P11.32) MUTATED     39   29
  DEL PEAK 35(18P11.32) WILD-TYPE  100   89
        clus
vv       DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE
  FEMALE                            39                             100
  MALE                              29                              89
[1] 2 2
[1] FALSE
D60V5, binary
                                 cls
clus                                0   1
  DEL PEAK 35(18P11.32) MUTATED    49  18
  DEL PEAK 35(18P11.32) WILD-TYPE 130  54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(18P11.32) MUTATED     49   18
  DEL PEAK 35(18P11.32) WILD-TYPE  130   54
     clus
vv    DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE
  NO                             49                             130
  YES                            18                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 35(18P11.32) MUTATED                             16             0
  DEL PEAK 35(18P11.32) WILD-TYPE                           43             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 35(18P11.32) MUTATED                                                                          0
  DEL PEAK 35(18P11.32) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  DEL PEAK 35(18P11.32) MUTATED                     29
  DEL PEAK 35(18P11.32) WILD-TYPE                   74
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 35(18P11.32) MUTATED                                                  3
  DEL PEAK 35(18P11.32) WILD-TYPE                                                6
                                 vv
clus                              MYXOFIBROSARCOMA
  DEL PEAK 35(18P11.32) MUTATED                  5
  DEL PEAK 35(18P11.32) WILD-TYPE               19
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 35(18P11.32) MUTATED                                                          6
  DEL PEAK 35(18P11.32) WILD-TYPE                                                       22
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 35(18P11.32) MUTATED                                          0
  DEL PEAK 35(18P11.32) WILD-TYPE                                        2
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 35(18P11.32) MUTATED                             0
  DEL PEAK 35(18P11.32) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 35(18P11.32) MUTATED                               0
  DEL PEAK 35(18P11.32) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 35(18P11.32) MUTATED                                            9
  DEL PEAK 35(18P11.32) WILD-TYPE                                         12
D60V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 35(18P11.32) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        16
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                29
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     3
  MYXOFIBROSARCOMA                                                                                     5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
                                                                          clus
vv                                                                         DEL PEAK 35(18P11.32) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          43
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  74
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       6
  MYXOFIBROSARCOMA                                                                                      19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              22
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(18P11.32) MUTATED    36  22   3   7
  DEL PEAK 35(18P11.32) WILD-TYPE 116  47   6  19
D60V7, multiclass
    clus
vv   DEL PEAK 35(18P11.32) MUTATED DEL PEAK 35(18P11.32) WILD-TYPE
  R0                            36                             116
  R1                            22                              47
  R2                             3                               6
  RX                             7                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(18P11.32) MUTATED       0                         6    60
  DEL PEAK 35(18P11.32) WILD-TYPE     6                        12   164
D60V8, multiclass
                           clus
vv                          DEL PEAK 35(18P11.32) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                60
                           clus
vv                          DEL PEAK 35(18P11.32) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                                 cls
clus                                0   1
  DEL PEAK 35(18P11.32) MUTATED     0  61
  DEL PEAK 35(18P11.32) WILD-TYPE   5 159
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(18P11.32) MUTATED      0   61
  DEL PEAK 35(18P11.32) WILD-TYPE    5  159
                        clus
vv                       DEL PEAK 35(18P11.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            61
                        clus
vv                       DEL PEAK 35(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             159
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 36(18Q23) MUTATION ANALYSIS
D61V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(18Q23) MUTATED    43  43
  DEL PEAK 36(18Q23) WILD-TYPE 116  55
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                          86                          171 
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                          43                           55 
$`DEL PEAK 36(18Q23) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB2P 
       31.53        16.18        67.20        34.36        15.22        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB36 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-IW-A3M6 
      106.45        13.28        60.00        32.15        12.62        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB 
       11.70        17.75         8.28         6.35        18.08       188.15 
TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3R-A8YX TCGA-DX-A1KX 
       26.17        35.08        44.91        42.84         0.56        68.61 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT 
       12.85        54.21        33.53         6.28         9.70        49.05 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K 
       44.68        31.86        51.02        10.68        85.45        45.99 
TCGA-DX-A48P TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6Z0 
       46.03        82.68        31.96         3.06        16.87        64.21 
TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BZ 
       62.20         9.34        61.97        27.95        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2Z TCGA-FX-A48G TCGA-HB-A2OT 
        1.15        17.79        66.74        50.40        19.89        67.63 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VF 
       33.30        80.48         3.22        25.22       171.09         1.05 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
      123.78         5.19        63.81        35.28        30.31        25.41 
TCGA-MB-A8JK TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
       21.73        13.08        46.82        48.59        10.52        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         3.88        22.82        25.35         8.61        19.63 
TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C4 
       13.41        12.46        84.79        22.62        26.43        20.65 
TCGA-X6-A8C5 TCGA-Z4-AAPG 
       50.86        15.98 

$`DEL PEAK 36(18Q23) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        34.68        75.32        17.95        14.43        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 
       15.85        40.60        22.85       101.98        30.51        84.66 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-QC-A6FX TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL 
      159.29        20.94        17.52        41.49        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        54.74        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        38.47        36.03        18.64        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R 
       32.71        45.11        18.54        85.02        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       35.77         4.54        14.99        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
       34.88         9.73        24.26        35.28        52.77        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB 
      108.82        59.84        37.58        15.95        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       28.96        36.85        26.99        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO 
       86.30       101.23        21.30        34.49        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       29.49        48.20        20.05        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F 
       40.77       150.35        40.44        60.66        19.43        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       15.72        65.98        86.10         9.21        77.88       106.55 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA 
       15.48         8.05        34.88         4.57         0.72         9.80 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 
       19.53         1.38        19.89        37.12        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       17.36        23.38        16.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       37.55        38.63        81.01        17.65         1.84        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX 
       32.75        13.22        10.72        11.93         4.80        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       30.84        35.18        19.17        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                        0.56                         0.49 
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                      188.15                       159.29 
  DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE 
                       25.79                        34.49 
[1] "0.6 - 188.2 (25.8)" "0.5 - 159.3 (34.5)"
[1] "hr=" "1.8"
D61V2, continuous
                              vv
clus                           CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 36(18Q23) MUTATED                0                  4
  DEL PEAK 36(18Q23) WILD-TYPE              1                  3
                              vv
clus                           CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 36(18Q23) MUTATED                     0                   0
  DEL PEAK 36(18Q23) WILD-TYPE                   2                   1
                              vv
clus                           CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 36(18Q23) MUTATED                               1
  DEL PEAK 36(18Q23) WILD-TYPE                             1
                              vv
clus                           GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 36(18Q23) MUTATED                       0                      7
  DEL PEAK 36(18Q23) WILD-TYPE                     1                     21
                              vv
clus                           HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 36(18Q23) MUTATED                      1                    0
  DEL PEAK 36(18Q23) WILD-TYPE                    1                    1
                              vv
clus                           HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 36(18Q23) MUTATED                                       0
  DEL PEAK 36(18Q23) WILD-TYPE                                     2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 36(18Q23) MUTATED                                  0
  DEL PEAK 36(18Q23) WILD-TYPE                                1
                              vv
clus                           LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 36(18Q23) MUTATED                                                0
  DEL PEAK 36(18Q23) WILD-TYPE                                              2
                              vv
clus                           LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 36(18Q23) MUTATED                                 3
  DEL PEAK 36(18Q23) WILD-TYPE                               7
                              vv
clus                           LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 36(18Q23) MUTATED                                         0
  DEL PEAK 36(18Q23) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 36(18Q23) MUTATED                              1
  DEL PEAK 36(18Q23) WILD-TYPE                            3
                              vv
clus                           LOWER EXTREMITY - GROIN
  DEL PEAK 36(18Q23) MUTATED                         1
  DEL PEAK 36(18Q23) WILD-TYPE                       1
                              vv
clus                           LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 36(18Q23) MUTATED                                  9
  DEL PEAK 36(18Q23) WILD-TYPE                                8
                              vv
clus                           LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 36(18Q23) MUTATED                                         3
  DEL PEAK 36(18Q23) WILD-TYPE                                       2
                              vv
clus                           LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 36(18Q23) MUTATED                             21
  DEL PEAK 36(18Q23) WILD-TYPE                           23
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 36(18Q23) MUTATED                                         1
  DEL PEAK 36(18Q23) WILD-TYPE                                       3
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 36(18Q23) MUTATED                                           1
  DEL PEAK 36(18Q23) WILD-TYPE                                         1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 36(18Q23) MUTATED                                                  1
  DEL PEAK 36(18Q23) WILD-TYPE                                                4
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 36(18Q23) MUTATED                                          2
  DEL PEAK 36(18Q23) WILD-TYPE                                        6
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 36(18Q23) MUTATED                                                         0
  DEL PEAK 36(18Q23) WILD-TYPE                                                       2
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 36(18Q23) MUTATED                                            0
  DEL PEAK 36(18Q23) WILD-TYPE                                          1
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 36(18Q23) MUTATED                                                  20
  DEL PEAK 36(18Q23) WILD-TYPE                                                53
                              vv
clus                           RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 36(18Q23) MUTATED                                                    1
  DEL PEAK 36(18Q23) WILD-TYPE                                                  2
                              vv
clus                           SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 36(18Q23) MUTATED                                    1
  DEL PEAK 36(18Q23) WILD-TYPE                                  1
                              vv
clus                           SUPERFICIAL TRUNK - BACK
  DEL PEAK 36(18Q23) MUTATED                          0
  DEL PEAK 36(18Q23) WILD-TYPE                        5
                              vv
clus                           SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 36(18Q23) MUTATED                             2
  DEL PEAK 36(18Q23) WILD-TYPE                           2
                              vv
clus                           SUPERFICIAL TRUNK - FLANK
  DEL PEAK 36(18Q23) MUTATED                           0
  DEL PEAK 36(18Q23) WILD-TYPE                         1
                              vv
clus                           UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 36(18Q23) MUTATED                                   3
  DEL PEAK 36(18Q23) WILD-TYPE                                 4
                              vv
clus                           UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 36(18Q23) MUTATED                                   2
  DEL PEAK 36(18Q23) WILD-TYPE                                 3
D61V3, multiclass
                                                         clus
vv                                                        DEL PEAK 36(18Q23) MUTATED
  CHEST - BREAST                                                                   0
  CHEST - CHEST WALL                                                               4
  CHEST - LUNG/PLEURA                                                              0
  CHEST - MEDIASTINUM                                                              0
  CHEST - OTHER (PLEASE SPECIFY                                                    1
  GYNECOLOGICAL - OVARY                                                            0
  GYNECOLOGICAL - UTERUS                                                           7
  HEAD AND NECK - HEAD                                                             1
  HEAD AND NECK - NECK                                                             0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                            0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                 0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                   0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                  3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                          0
  LOWER EXTREMITY - FOOT/ANKLE                                                     1
  LOWER EXTREMITY - GROIN                                                          1
  LOWER EXTREMITY - LOWER LEG/CALF                                                 9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                          3
  LOWER EXTREMITY - THIGH/KNEE                                                    21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                 1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                          0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                       0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                               20
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                               1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                               1
  SUPERFICIAL TRUNK - BACK                                                         0
  SUPERFICIAL TRUNK - BUTTOCK                                                      2
  SUPERFICIAL TRUNK - FLANK                                                        0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                2
                                                         clus
vv                                                        DEL PEAK 36(18Q23) WILD-TYPE
  CHEST - BREAST                                                                     1
  CHEST - CHEST WALL                                                                 3
  CHEST - LUNG/PLEURA                                                                2
  CHEST - MEDIASTINUM                                                                1
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              1
  GYNECOLOGICAL - UTERUS                                                            21
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            2
  LOWER EXTREMITY - FOOT/ANKLE                                                       3
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                      23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 53
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           5
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                              cls
clus                            0  1
  DEL PEAK 36(18Q23) MUTATED   50 36
  DEL PEAK 36(18Q23) WILD-TYPE 89 82
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(18Q23) MUTATED     50   36
  DEL PEAK 36(18Q23) WILD-TYPE   89   82
        clus
vv       DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE
  FEMALE                         50                           89
  MALE                           36                           82
[1] 2 2
[1] FALSE
D61V5, binary
                              cls
clus                             0   1
  DEL PEAK 36(18Q23) MUTATED    55  30
  DEL PEAK 36(18Q23) WILD-TYPE 124  42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(18Q23) MUTATED     55   30
  DEL PEAK 36(18Q23) WILD-TYPE  124   42
     clus
vv    DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE
  NO                          55                          124
  YES                         30                           42
[1] 2 2
[1] FALSE
                              vv
clus                           DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 36(18Q23) MUTATED                             16             0
  DEL PEAK 36(18Q23) WILD-TYPE                           43             2
                              vv
clus                           GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 36(18Q23) MUTATED                                                                          0
  DEL PEAK 36(18Q23) WILD-TYPE                                                                        1
                              vv
clus                           LEIOMYOSARCOMA (LMS)
  DEL PEAK 36(18Q23) MUTATED                     28
  DEL PEAK 36(18Q23) WILD-TYPE                   75
                              vv
clus                           MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 36(18Q23) MUTATED                                                  6
  DEL PEAK 36(18Q23) WILD-TYPE                                                3
                              vv
clus                           MYXOFIBROSARCOMA
  DEL PEAK 36(18Q23) MUTATED                  9
  DEL PEAK 36(18Q23) WILD-TYPE               15
                              vv
clus                           PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 36(18Q23) MUTATED                                                         15
  DEL PEAK 36(18Q23) WILD-TYPE                                                       13
                              vv
clus                           SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 36(18Q23) MUTATED                                          0
  DEL PEAK 36(18Q23) WILD-TYPE                                        2
                              vv
clus                           SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 36(18Q23) MUTATED                             0
  DEL PEAK 36(18Q23) WILD-TYPE                           2
                              vv
clus                           SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 36(18Q23) MUTATED                               0
  DEL PEAK 36(18Q23) WILD-TYPE                             6
                              vv
clus                           UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 36(18Q23) MUTATED                                           12
  DEL PEAK 36(18Q23) WILD-TYPE                                          9
D61V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 36(18Q23) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                     16
  DESMOID TUMOR                                                                                     0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                          0
  LEIOMYOSARCOMA (LMS)                                                                             28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                  6
  MYXOFIBROSARCOMA                                                                                  9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                         15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                          0
  SYNOVIAL SARCOMA - BIPHASIC                                                                       0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                     0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                       12
                                                                          clus
vv                                                                         DEL PEAK 36(18Q23) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                       43
  DESMOID TUMOR                                                                                       2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            1
  LEIOMYOSARCOMA (LMS)                                                                               75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                   15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            2
  SYNOVIAL SARCOMA - BIPHASIC                                                                         2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 36(18Q23) MUTATED    45  25   4  11
  DEL PEAK 36(18Q23) WILD-TYPE 107  44   5  15
D61V7, multiclass
    clus
vv   DEL PEAK 36(18Q23) MUTATED DEL PEAK 36(18Q23) WILD-TYPE
  R0                         45                          107
  R1                         25                           44
  R2                          4                            5
  RX                         11                           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(18Q23) MUTATED       2                         6    74
  DEL PEAK 36(18Q23) WILD-TYPE     4                        12   150
D61V8, multiclass
                           clus
vv                          DEL PEAK 36(18Q23) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             74
                           clus
vv                          DEL PEAK 36(18Q23) WILD-TYPE
  ASIAN                                                4
  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"
D61V9, binary
                              cls
clus                             0   1
  DEL PEAK 36(18Q23) MUTATED     1  75
  DEL PEAK 36(18Q23) WILD-TYPE   4 145
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(18Q23) MUTATED      1   75
  DEL PEAK 36(18Q23) WILD-TYPE    4  145
                        clus
vv                       DEL PEAK 36(18Q23) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         75
                        clus
vv                       DEL PEAK 36(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          145
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 37(19P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(19P13.3) MUTATED    43  27
  DEL PEAK 37(19P13.3) WILD-TYPE 116  71
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                            70                            187 
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                            27                             71 
$`DEL PEAK 37(19P13.3) MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2W 
       34.68        67.20        34.36        17.95        14.07       106.45 
TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        37.02        12.62        52.11        26.93        52.27 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HU 
       22.62        11.70         6.35        19.69        68.55        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3UC TCGA-DX-A3UF 
       42.84        10.32       136.44        51.02        68.55        85.45 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6YX TCGA-DX-A6Z0 
       26.47        15.95        37.41        82.68        16.87        64.21 
TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-FX-A48G TCGA-FX-A76Y 
       62.20         9.34        38.17        40.77        19.89        15.48 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
       33.30         0.72        19.53        19.89        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RV 
       13.58         5.92         1.05       101.26        62.17         5.19 
TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VB 
       30.31         7.36        81.01        13.08        17.65        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       37.12       111.98        16.77        18.94         3.88        22.82 
TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       32.75        10.72        11.93        38.27        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 
       35.90        18.08        45.34        20.65 

$`DEL PEAK 37(19P13.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        31.53        16.18        75.32        15.22        14.43 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       15.85        40.60        12.07        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-IS-A3K6 TCGA-IS-A3K8 
       30.51        60.00        84.66        16.60        28.21       159.29 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       17.75         8.28        18.08        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HR 
       26.17        41.49        35.08        50.01        53.49        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       44.91        54.74        14.37        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       26.56         0.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83        33.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        10.68        73.87        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
      108.82        59.84        37.58        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       36.85        26.99         3.06        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO 
       86.30       101.23        21.30        34.49        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       29.49        48.20        20.05        61.97        45.14        47.87 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      150.35        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
        6.58         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV 
        8.05        67.63        34.88         4.57         9.80        80.48 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
        3.22         1.38        37.12        85.97        16.41         3.91 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33       123.78        17.36        23.38        63.81        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       35.28        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57        10.45       122.96        37.55 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VD 
       38.63         1.84        46.82        18.08        35.90       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
       64.77        10.52         0.72        25.35         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WP-A9GB 
       13.22        13.41        12.46         4.80        84.79         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       63.35        26.43        30.84        35.18        19.17        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                          0.72                           0.49 
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                        171.09                         188.15 
  DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE 
                         26.70                          31.86 
[1] "0.7 - 171.1 (26.7)" "0.5 - 188.2 (31.9)"
[1] "hr=" "1.1"
D62V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 37(19P13.3) MUTATED                0                  4
  DEL PEAK 37(19P13.3) WILD-TYPE              1                  3
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 37(19P13.3) MUTATED                     0                   0
  DEL PEAK 37(19P13.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 37(19P13.3) MUTATED                               1
  DEL PEAK 37(19P13.3) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 37(19P13.3) MUTATED                       0                     14
  DEL PEAK 37(19P13.3) WILD-TYPE                     1                     14
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 37(19P13.3) MUTATED                      1                    0
  DEL PEAK 37(19P13.3) WILD-TYPE                    1                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 37(19P13.3) MUTATED                                       0
  DEL PEAK 37(19P13.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 37(19P13.3) MUTATED                                  0
  DEL PEAK 37(19P13.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 37(19P13.3) MUTATED                                                0
  DEL PEAK 37(19P13.3) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 37(19P13.3) MUTATED                                 2
  DEL PEAK 37(19P13.3) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 37(19P13.3) MUTATED                                         0
  DEL PEAK 37(19P13.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 37(19P13.3) MUTATED                              1
  DEL PEAK 37(19P13.3) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 37(19P13.3) MUTATED                         1
  DEL PEAK 37(19P13.3) WILD-TYPE                       1
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 37(19P13.3) MUTATED                                  4
  DEL PEAK 37(19P13.3) WILD-TYPE                               13
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 37(19P13.3) MUTATED                                         3
  DEL PEAK 37(19P13.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 37(19P13.3) MUTATED                             15
  DEL PEAK 37(19P13.3) WILD-TYPE                           29
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 37(19P13.3) MUTATED                                         2
  DEL PEAK 37(19P13.3) WILD-TYPE                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 37(19P13.3) MUTATED                                           0
  DEL PEAK 37(19P13.3) WILD-TYPE                                         2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 37(19P13.3) MUTATED                                                  0
  DEL PEAK 37(19P13.3) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 37(19P13.3) MUTATED                                          2
  DEL PEAK 37(19P13.3) WILD-TYPE                                        6
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 37(19P13.3) MUTATED                                                         0
  DEL PEAK 37(19P13.3) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 37(19P13.3) MUTATED                                            1
  DEL PEAK 37(19P13.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 37(19P13.3) MUTATED                                                  14
  DEL PEAK 37(19P13.3) WILD-TYPE                                                59
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 37(19P13.3) MUTATED                                                    1
  DEL PEAK 37(19P13.3) WILD-TYPE                                                  2
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 37(19P13.3) MUTATED                                    0
  DEL PEAK 37(19P13.3) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 37(19P13.3) MUTATED                          0
  DEL PEAK 37(19P13.3) WILD-TYPE                        5
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 37(19P13.3) MUTATED                             2
  DEL PEAK 37(19P13.3) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 37(19P13.3) MUTATED                           0
  DEL PEAK 37(19P13.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 37(19P13.3) MUTATED                                   2
  DEL PEAK 37(19P13.3) WILD-TYPE                                 5
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 37(19P13.3) MUTATED                                   0
  DEL PEAK 37(19P13.3) WILD-TYPE                                 5
D62V3, multiclass
                                                         clus
vv                                                        DEL PEAK 37(19P13.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 4
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                            14
  HEAD AND NECK - HEAD                                                               1
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                                   4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            3
  LOWER EXTREMITY - THIGH/KNEE                                                      15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  0
                                                         clus
vv                                                        DEL PEAK 37(19P13.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   3
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              14
  HEAD AND NECK - HEAD                                                                 1
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                                    13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              2
  LOWER EXTREMITY - THIGH/KNEE                                                        29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                                cls
clus                              0  1
  DEL PEAK 37(19P13.3) MUTATED   47 23
  DEL PEAK 37(19P13.3) WILD-TYPE 92 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(19P13.3) MUTATED     47   23
  DEL PEAK 37(19P13.3) WILD-TYPE   92   95
        clus
vv       DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE
  FEMALE                           47                             92
  MALE                             23                             95
[1] 2 2
[1] FALSE
D62V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(19P13.3) MUTATED    49  21
  DEL PEAK 37(19P13.3) WILD-TYPE 130  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(19P13.3) MUTATED     49   21
  DEL PEAK 37(19P13.3) WILD-TYPE  130   51
     clus
vv    DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE
  NO                            49                            130
  YES                           21                             51
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 37(19P13.3) MUTATED                              6             0
  DEL PEAK 37(19P13.3) WILD-TYPE                           53             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 37(19P13.3) MUTATED                                                                          0
  DEL PEAK 37(19P13.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 37(19P13.3) MUTATED                     43
  DEL PEAK 37(19P13.3) WILD-TYPE                   60
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 37(19P13.3) MUTATED                                                  3
  DEL PEAK 37(19P13.3) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 37(19P13.3) MUTATED                  6
  DEL PEAK 37(19P13.3) WILD-TYPE               18
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 37(19P13.3) MUTATED                                                          7
  DEL PEAK 37(19P13.3) WILD-TYPE                                                       21
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 37(19P13.3) MUTATED                                          0
  DEL PEAK 37(19P13.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 37(19P13.3) MUTATED                             0
  DEL PEAK 37(19P13.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 37(19P13.3) MUTATED                               0
  DEL PEAK 37(19P13.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 37(19P13.3) MUTATED                                            5
  DEL PEAK 37(19P13.3) WILD-TYPE                                         16
D62V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 37(19P13.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        6
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               43
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                    6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          5
                                                                          clus
vv                                                                         DEL PEAK 37(19P13.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         53
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 60
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           16
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(19P13.3) MUTATED    40  18   2   9
  DEL PEAK 37(19P13.3) WILD-TYPE 112  51   7  17
D62V7, multiclass
    clus
vv   DEL PEAK 37(19P13.3) MUTATED DEL PEAK 37(19P13.3) WILD-TYPE
  R0                           40                            112
  R1                           18                             51
  R2                            2                              7
  RX                            9                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(19P13.3) MUTATED       1                         6    59
  DEL PEAK 37(19P13.3) WILD-TYPE     5                        12   165
D62V8, multiclass
                           clus
vv                          DEL PEAK 37(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               59
                           clus
vv                          DEL PEAK 37(19P13.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             12
  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"
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(19P13.3) MUTATED     0  60
  DEL PEAK 37(19P13.3) WILD-TYPE   5 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(19P13.3) MUTATED      0   60
  DEL PEAK 37(19P13.3) WILD-TYPE    5  160
                        clus
vv                       DEL PEAK 37(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 37(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            160
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 38(19Q13.43) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 38(19Q13.43) MUTATED   71 35
  DEL PEAK 38(19Q13.43) WILD-TYPE 88 63
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                            106                             151 
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                             35                              63 
$`DEL PEAK 38(19Q13.43) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-AB2W TCGA-DX-AB36 
       16.18        67.20        75.32        15.22       106.45        60.00 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-LI-A9QH 
       32.15        16.60        12.62        52.27        22.62        17.75 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HI 
       18.08        20.94       188.15        17.52        26.17        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY 
       19.69        53.49        68.55        44.91        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2J0 
       38.47        36.03        32.71        12.85        74.66         9.70 
TCGA-DX-A3LT TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48U 
       49.05        50.43        24.26        35.28        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BH TCGA-DX-A6YR 
       59.84        37.58        37.41        82.68        26.99        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        50.50        86.30       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       62.20        30.35        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O 
       40.77       150.35        40.44         1.15        12.00        86.10 
TCGA-DX-AB2Q TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       66.74        49.15        21.70        20.32        19.89        15.48 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IS-A3KA 
        4.57        33.30         9.80        80.48         3.22        13.58 
TCGA-IW-A3M4 TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU 
       85.97       101.26       123.78        23.38        63.81        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DO 
       30.31        25.41        21.73         7.36       122.96        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ 
       13.08        17.65        46.82        35.90        10.52        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G 
       18.94         3.88        22.82         8.61        19.63        10.72 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       12.46        22.62        26.43        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-Z4-AAPG 
       35.18        20.65        50.86        15.98 

$`DEL PEAK 38(19Q13.43) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BH 
       36.30        31.53        34.68        34.36        17.95        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        15.85        40.60        12.07        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH 
      101.98        30.51        84.66        37.02        52.11        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-WK-A8XT 
       28.21       159.29        11.70         8.28         6.35        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 
       35.08        88.57        54.74        14.37        42.84        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 
       26.56         0.56        14.04        68.61        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         8.58        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        34.88        85.45         9.73        45.99 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       52.77        26.47        15.95        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EO TCGA-DX-A7EQ 
       36.85         3.06        16.87        64.21       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       48.20        20.05         9.34        27.95        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S 
       19.43         6.58        17.79        15.72        65.98         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       77.88       106.55        50.40        50.89        71.31        31.13 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK 
        8.05        67.63        34.88         0.72        19.53         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE 
       19.89        37.12        25.22       171.09         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV 
        1.05         3.91        53.33        62.17        17.36         5.19 
TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       16.41         0.49        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       11.57        10.45        37.55        38.63         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        37.12       130.32       111.98        64.77         0.72 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
       25.35        32.75        13.22        13.41        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WC 
       84.79        38.27        65.46         8.58        63.35        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                           1.15                            0.49 
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                         188.15                          171.09 
  DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE 
                         33.005                          29.490 
[1] "1.1 - 188.2 (33.0)" "0.5 - 171.1 (29.5)"
[1] "hr=" "1.4"
D63V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 38(19Q13.43) MUTATED                0                  3
  DEL PEAK 38(19Q13.43) WILD-TYPE              1                  4
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 38(19Q13.43) MUTATED                     0                   1
  DEL PEAK 38(19Q13.43) WILD-TYPE                   2                   0
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 38(19Q13.43) MUTATED                               2
  DEL PEAK 38(19Q13.43) WILD-TYPE                             0
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 38(19Q13.43) MUTATED                       1                     12
  DEL PEAK 38(19Q13.43) WILD-TYPE                     0                     16
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 38(19Q13.43) MUTATED                      1                    0
  DEL PEAK 38(19Q13.43) WILD-TYPE                    1                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 38(19Q13.43) MUTATED                                       0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 38(19Q13.43) MUTATED                                  0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 38(19Q13.43) MUTATED                                                0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                              2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 38(19Q13.43) MUTATED                                 2
  DEL PEAK 38(19Q13.43) WILD-TYPE                               8
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 38(19Q13.43) MUTATED                                         0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 38(19Q13.43) MUTATED                              0
  DEL PEAK 38(19Q13.43) WILD-TYPE                            4
                                 vv
clus                              LOWER EXTREMITY - GROIN
  DEL PEAK 38(19Q13.43) MUTATED                         0
  DEL PEAK 38(19Q13.43) WILD-TYPE                       2
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 38(19Q13.43) MUTATED                                 10
  DEL PEAK 38(19Q13.43) WILD-TYPE                                7
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 38(19Q13.43) MUTATED                                         3
  DEL PEAK 38(19Q13.43) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 38(19Q13.43) MUTATED                             21
  DEL PEAK 38(19Q13.43) WILD-TYPE                           23
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 38(19Q13.43) MUTATED                                         2
  DEL PEAK 38(19Q13.43) WILD-TYPE                                       2
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 38(19Q13.43) MUTATED                                           1
  DEL PEAK 38(19Q13.43) WILD-TYPE                                         1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 38(19Q13.43) MUTATED                                                  0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                5
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 38(19Q13.43) MUTATED                                          4
  DEL PEAK 38(19Q13.43) WILD-TYPE                                        4
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 38(19Q13.43) MUTATED                                                         2
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                       0
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 38(19Q13.43) MUTATED                                            0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                          1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 38(19Q13.43) MUTATED                                                  29
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                44
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 38(19Q13.43) MUTATED                                                    1
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                  2
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 38(19Q13.43) MUTATED                                    1
  DEL PEAK 38(19Q13.43) WILD-TYPE                                  1
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  DEL PEAK 38(19Q13.43) MUTATED                          1
  DEL PEAK 38(19Q13.43) WILD-TYPE                        4
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 38(19Q13.43) MUTATED                             2
  DEL PEAK 38(19Q13.43) WILD-TYPE                           2
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  DEL PEAK 38(19Q13.43) MUTATED                           0
  DEL PEAK 38(19Q13.43) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 38(19Q13.43) MUTATED                                   3
  DEL PEAK 38(19Q13.43) WILD-TYPE                                 4
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 38(19Q13.43) MUTATED                                   4
  DEL PEAK 38(19Q13.43) WILD-TYPE                                 1
D63V3, multiclass
                                                         clus
vv                                                        DEL PEAK 38(19Q13.43) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  3
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             12
  HEAD AND NECK - HEAD                                                                1
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        0
  LOWER EXTREMITY - GROIN                                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  29
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  1
  SUPERFICIAL TRUNK - BACK                                                            1
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
                                                         clus
vv                                                        DEL PEAK 38(19Q13.43) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    4
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                                         0
  GYNECOLOGICAL - OVARY                                                                 0
  GYNECOLOGICAL - UTERUS                                                               16
  HEAD AND NECK - HEAD                                                                  1
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          4
  LOWER EXTREMITY - GROIN                                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                                      7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               2
  LOWER EXTREMITY - THIGH/KNEE                                                         23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    44
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    1
  SUPERFICIAL TRUNK - BACK                                                              4
  SUPERFICIAL TRUNK - BUTTOCK                                                           2
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     1
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                                 cls
clus                               0  1
  DEL PEAK 38(19Q13.43) MUTATED   62 44
  DEL PEAK 38(19Q13.43) WILD-TYPE 77 74
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(19Q13.43) MUTATED     62   44
  DEL PEAK 38(19Q13.43) WILD-TYPE   77   74
        clus
vv       DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE
  FEMALE                            62                              77
  MALE                              44                              74
[1] 2 2
[1] FALSE
D63V5, binary
                                 cls
clus                                0   1
  DEL PEAK 38(19Q13.43) MUTATED    66  39
  DEL PEAK 38(19Q13.43) WILD-TYPE 113  33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(19Q13.43) MUTATED     66   39
  DEL PEAK 38(19Q13.43) WILD-TYPE  113   33
     clus
vv    DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE
  NO                             66                             113
  YES                            39                              33
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 38(19Q13.43) MUTATED                             17             0
  DEL PEAK 38(19Q13.43) WILD-TYPE                           42             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 38(19Q13.43) MUTATED                                                                          0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  DEL PEAK 38(19Q13.43) MUTATED                     43
  DEL PEAK 38(19Q13.43) WILD-TYPE                   60
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 38(19Q13.43) MUTATED                                                  5
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                4
                                 vv
clus                              MYXOFIBROSARCOMA
  DEL PEAK 38(19Q13.43) MUTATED                  8
  DEL PEAK 38(19Q13.43) WILD-TYPE               16
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 38(19Q13.43) MUTATED                                                         18
  DEL PEAK 38(19Q13.43) WILD-TYPE                                                       10
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 38(19Q13.43) MUTATED                                          0
  DEL PEAK 38(19Q13.43) WILD-TYPE                                        2
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 38(19Q13.43) MUTATED                             0
  DEL PEAK 38(19Q13.43) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 38(19Q13.43) MUTATED                               0
  DEL PEAK 38(19Q13.43) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 38(19Q13.43) MUTATED                                           15
  DEL PEAK 38(19Q13.43) WILD-TYPE                                          6
D63V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 38(19Q13.43) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        17
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                43
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                     8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          15
                                                                          clus
vv                                                                         DEL PEAK 38(19Q13.43) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          42
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  60
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       4
  MYXOFIBROSARCOMA                                                                                      16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                             6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 38(19Q13.43) MUTATED   59 32  1 13
  DEL PEAK 38(19Q13.43) WILD-TYPE 93 37  8 13
D63V7, multiclass
    clus
vv   DEL PEAK 38(19Q13.43) MUTATED DEL PEAK 38(19Q13.43) WILD-TYPE
  R0                            59                              93
  R1                            32                              37
  R2                             1                               8
  RX                            13                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(19Q13.43) MUTATED       1                         6    97
  DEL PEAK 38(19Q13.43) WILD-TYPE     5                        12   127
D63V8, multiclass
                           clus
vv                          DEL PEAK 38(19Q13.43) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                97
                           clus
vv                          DEL PEAK 38(19Q13.43) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              12
  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"
D63V9, binary
                                 cls
clus                                0   1
  DEL PEAK 38(19Q13.43) MUTATED     1  97
  DEL PEAK 38(19Q13.43) WILD-TYPE   4 123
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(19Q13.43) MUTATED      1   97
  DEL PEAK 38(19Q13.43) WILD-TYPE    4  123
                        clus
vv                       DEL PEAK 38(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            97
                        clus
vv                       DEL PEAK 38(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             123
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 39(21Q11.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(21Q11.2) MUTATED    32  19
  DEL PEAK 39(21Q11.2) WILD-TYPE 127  79
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                            51                            206 
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                            19                             79 
$`DEL PEAK 39(21Q11.2) MUTATED`
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB32 TCGA-HB-A43Z TCGA-QQ-A8VB TCGA-SG-A849 
       17.95        14.43       101.98        37.02       188.15        17.52 
TCGA-VT-A80J TCGA-3B-A9HL TCGA-3B-A9HR TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
       26.17        19.69        88.57        18.54        85.02        74.66 
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A48R 
        6.28        33.44        44.68        31.86        10.68        26.47 
TCGA-DX-A48V TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO 
       59.84         3.06        16.87         9.34        47.87        40.77 
TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IS-A3K7 
        6.58        86.10        66.74        20.32        67.63       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
        5.92        16.41         1.05         3.91       101.26        62.17 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-PC-A5DO TCGA-QQ-A8VG TCGA-QQ-A8VH 
        5.19        63.81        35.28        81.01        64.77        10.52 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       16.77        18.94         8.61        19.63        13.41        10.72 
TCGA-WK-A8XS TCGA-X6-A8C2 TCGA-Z4-AAPG 
       84.79        35.18        15.98 

$`DEL PEAK 39(21Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        15.22        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        22.85        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       28.21       159.29        22.62        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
        6.35        18.08        20.94        41.49        35.08        50.01 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        68.61        12.85        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U7 
        9.04        49.05        86.83       136.44        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       46.03       108.82        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       36.33        28.96        31.96        36.85        26.99        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        50.50        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS 
       20.05        61.97        45.14        38.17       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       40.44        36.69        60.66        19.43         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       12.00        15.72        65.98         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       19.89        15.48         8.05        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-K1-A3PO 
       19.89        37.12        25.22        13.58        85.97        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
      123.78        17.36        23.38        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       13.08        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-RN-A68Q TCGA-SG-A6Z7 
       35.90        37.12       130.32       111.98         0.72         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-AB3D TCGA-WK-A8XO 
       22.82        25.35        32.75        13.22        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        38.27        65.46        22.62         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       26.43        35.90        18.08        45.34        30.84        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                          1.05                           0.49 
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE 
                        26.170                         31.745 
[1] "1.1 - 188.2 (26.2)" "0.5 - 159.3 (31.7)"
[1] "hr=" "1.1"
D64V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 39(21Q11.2) MUTATED                0                  2
  DEL PEAK 39(21Q11.2) WILD-TYPE              1                  5
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 39(21Q11.2) MUTATED                     0                   0
  DEL PEAK 39(21Q11.2) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 39(21Q11.2) MUTATED                               1
  DEL PEAK 39(21Q11.2) WILD-TYPE                             1
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 39(21Q11.2) MUTATED                       0                      7
  DEL PEAK 39(21Q11.2) WILD-TYPE                     1                     21
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 39(21Q11.2) MUTATED                      0                    0
  DEL PEAK 39(21Q11.2) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 39(21Q11.2) MUTATED                                       0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 39(21Q11.2) MUTATED                                  0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 39(21Q11.2) MUTATED                                                0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 39(21Q11.2) MUTATED                                 2
  DEL PEAK 39(21Q11.2) WILD-TYPE                               8
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 39(21Q11.2) MUTATED                                         0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 39(21Q11.2) MUTATED                              1
  DEL PEAK 39(21Q11.2) WILD-TYPE                            3
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 39(21Q11.2) MUTATED                         0
  DEL PEAK 39(21Q11.2) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 39(21Q11.2) MUTATED                                  5
  DEL PEAK 39(21Q11.2) WILD-TYPE                               12
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 39(21Q11.2) MUTATED                                         2
  DEL PEAK 39(21Q11.2) WILD-TYPE                                       3
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 39(21Q11.2) MUTATED                              9
  DEL PEAK 39(21Q11.2) WILD-TYPE                           35
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 39(21Q11.2) MUTATED                                         0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                       4
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 39(21Q11.2) MUTATED                                           1
  DEL PEAK 39(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 39(21Q11.2) MUTATED                                                  0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 39(21Q11.2) MUTATED                                          0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                        8
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 39(21Q11.2) MUTATED                                                         0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                       2
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 39(21Q11.2) MUTATED                                            1
  DEL PEAK 39(21Q11.2) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 39(21Q11.2) MUTATED                                                  13
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                60
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 39(21Q11.2) MUTATED                                                    0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 39(21Q11.2) MUTATED                                    1
  DEL PEAK 39(21Q11.2) WILD-TYPE                                  1
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 39(21Q11.2) MUTATED                          1
  DEL PEAK 39(21Q11.2) WILD-TYPE                        4
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 39(21Q11.2) MUTATED                             2
  DEL PEAK 39(21Q11.2) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 39(21Q11.2) MUTATED                           0
  DEL PEAK 39(21Q11.2) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 39(21Q11.2) MUTATED                                   2
  DEL PEAK 39(21Q11.2) WILD-TYPE                                 5
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 39(21Q11.2) MUTATED                                   1
  DEL PEAK 39(21Q11.2) WILD-TYPE                                 4
D64V3, multiclass
                                                         clus
vv                                                        DEL PEAK 39(21Q11.2) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      1
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             7
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       1
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            2
  LOWER EXTREMITY - THIGH/KNEE                                                       9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 1
  SUPERFICIAL TRUNK - BACK                                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        DEL PEAK 39(21Q11.2) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   5
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        1
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              21
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         3
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              3
  LOWER EXTREMITY - THIGH/KNEE                                                        35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   1
  SUPERFICIAL TRUNK - BACK                                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                                cls
clus                               0   1
  DEL PEAK 39(21Q11.2) MUTATED    30  21
  DEL PEAK 39(21Q11.2) WILD-TYPE 109  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(21Q11.2) MUTATED     30   21
  DEL PEAK 39(21Q11.2) WILD-TYPE  109   97
        clus
vv       DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE
  FEMALE                           30                            109
  MALE                             21                             97
[1] 2 2
[1] FALSE
D64V5, binary
                                cls
clus                               0   1
  DEL PEAK 39(21Q11.2) MUTATED    33  18
  DEL PEAK 39(21Q11.2) WILD-TYPE 146  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(21Q11.2) MUTATED     33   18
  DEL PEAK 39(21Q11.2) WILD-TYPE  146   54
     clus
vv    DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE
  NO                            33                            146
  YES                           18                             54
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 39(21Q11.2) MUTATED                              8             0
  DEL PEAK 39(21Q11.2) WILD-TYPE                           51             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 39(21Q11.2) MUTATED                                                                          0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 39(21Q11.2) MUTATED                     18
  DEL PEAK 39(21Q11.2) WILD-TYPE                   85
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 39(21Q11.2) MUTATED                                                  5
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                4
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 39(21Q11.2) MUTATED                  4
  DEL PEAK 39(21Q11.2) WILD-TYPE               20
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 39(21Q11.2) MUTATED                                                          7
  DEL PEAK 39(21Q11.2) WILD-TYPE                                                       21
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 39(21Q11.2) MUTATED                                          0
  DEL PEAK 39(21Q11.2) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 39(21Q11.2) MUTATED                             0
  DEL PEAK 39(21Q11.2) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 39(21Q11.2) MUTATED                               0
  DEL PEAK 39(21Q11.2) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 39(21Q11.2) MUTATED                                            9
  DEL PEAK 39(21Q11.2) WILD-TYPE                                         12
D64V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 39(21Q11.2) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        8
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               18
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    5
  MYXOFIBROSARCOMA                                                                                    4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          9
                                                                          clus
vv                                                                         DEL PEAK 39(21Q11.2) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         51
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 85
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      4
  MYXOFIBROSARCOMA                                                                                     20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(21Q11.2) MUTATED    28  15   3   4
  DEL PEAK 39(21Q11.2) WILD-TYPE 124  54   6  22
D64V7, multiclass
    clus
vv   DEL PEAK 39(21Q11.2) MUTATED DEL PEAK 39(21Q11.2) WILD-TYPE
  R0                           28                            124
  R1                           15                             54
  R2                            3                              6
  RX                            4                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(21Q11.2) MUTATED       1                         5    43
  DEL PEAK 39(21Q11.2) WILD-TYPE     5                        13   181
D64V8, multiclass
                           clus
vv                          DEL PEAK 39(21Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               43
                           clus
vv                          DEL PEAK 39(21Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(21Q11.2) MUTATED     2  43
  DEL PEAK 39(21Q11.2) WILD-TYPE   3 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(21Q11.2) MUTATED      2   43
  DEL PEAK 39(21Q11.2) WILD-TYPE    3  177
                        clus
vv                       DEL PEAK 39(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       DEL PEAK 39(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            177
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 40(21Q22.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(21Q22.3) MUTATED    40  26
  DEL PEAK 40(21Q22.3) WILD-TYPE 119  72
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                            66                            191 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                            26                             72 
$`DEL PEAK 40(21Q22.3) MUTATED`
TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2X TCGA-DX-AB32 TCGA-IF-A4AK TCGA-IW-A3M6 
       17.95        15.85        13.28       101.98        52.27        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       11.70        17.75        18.08        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KX 
       26.17        35.08        19.69        44.91        14.04        68.61 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LW 
       18.54        85.02        74.66         6.28         9.70       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB 
       33.44        44.68        31.86        85.45        24.26        36.33 
TCGA-DX-A6BF TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       31.96        16.87        21.30         9.34        45.14        47.87 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2Q 
       27.95        36.69         6.58         1.15        86.10        66.74 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K7 
       49.15        20.32        67.63         3.22        25.22       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QU 
        5.92        16.41       101.26        62.17        23.38        35.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
        0.49        21.73        64.77        16.77        18.94         3.88 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        8.61        10.72        84.79        45.34        30.84        35.18 

$`DEL PEAK 40(21Q22.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        15.22        14.43        14.07        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
      106.45        22.85        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 
       16.60        37.02        12.62        52.11        26.93        28.21 
TCGA-IS-A3K8 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP 
      159.29         8.28         6.35        41.49        50.01        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       68.55        88.57        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        18.64        26.56         0.56 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        12.85        45.11        54.21        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U6 
       95.38        79.17         9.04        49.05        86.83        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       50.43        34.88         9.73        45.99        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       37.41        82.68        28.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        50.50        86.30        64.21       101.23 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       20.05        61.97        38.17        40.77       150.35        40.44 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43        17.79        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       31.13        21.70        19.89        15.48         8.05        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF 
        1.38        19.89        37.12        13.58        85.97         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS 
        3.91        53.33       123.78        17.36         5.19        63.81 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       16.41        30.31        25.41        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       10.52         0.72        22.82        25.35        32.75        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX 
       13.22        13.41        12.46        11.93         4.80        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       65.46        22.62         8.58        63.35        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       18.08        19.17        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                          0.49                           0.56 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                        188.15                         159.29 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                        25.695                         32.710 
[1] "0.5 - 188.2 (25.7)" "0.6 - 159.3 (32.7)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 40(21Q22.3) MUTATED                0                  2
  DEL PEAK 40(21Q22.3) WILD-TYPE              1                  5
                                vv
clus                             CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 40(21Q22.3) MUTATED                     0                   0
  DEL PEAK 40(21Q22.3) WILD-TYPE                   2                   1
                                vv
clus                             CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 40(21Q22.3) MUTATED                               0
  DEL PEAK 40(21Q22.3) WILD-TYPE                             2
                                vv
clus                             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 40(21Q22.3) MUTATED                       0                      6
  DEL PEAK 40(21Q22.3) WILD-TYPE                     1                     22
                                vv
clus                             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 40(21Q22.3) MUTATED                      0                    0
  DEL PEAK 40(21Q22.3) WILD-TYPE                    2                    1
                                vv
clus                             HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 40(21Q22.3) MUTATED                                       0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                     2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 40(21Q22.3) MUTATED                                  0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                1
                                vv
clus                             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 40(21Q22.3) MUTATED                                                0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                              2
                                vv
clus                             LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 40(21Q22.3) MUTATED                                 3
  DEL PEAK 40(21Q22.3) WILD-TYPE                               7
                                vv
clus                             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 40(21Q22.3) MUTATED                                         0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                       2
                                vv
clus                             LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 40(21Q22.3) MUTATED                              0
  DEL PEAK 40(21Q22.3) WILD-TYPE                            4
                                vv
clus                             LOWER EXTREMITY - GROIN
  DEL PEAK 40(21Q22.3) MUTATED                         0
  DEL PEAK 40(21Q22.3) WILD-TYPE                       2
                                vv
clus                             LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 40(21Q22.3) MUTATED                                  9
  DEL PEAK 40(21Q22.3) WILD-TYPE                                8
                                vv
clus                             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 40(21Q22.3) MUTATED                                         1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                       4
                                vv
clus                             LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 40(21Q22.3) MUTATED                             15
  DEL PEAK 40(21Q22.3) WILD-TYPE                           29
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 40(21Q22.3) MUTATED                                         1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                       3
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 40(21Q22.3) MUTATED                                           1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                         1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 40(21Q22.3) MUTATED                                                  0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                5
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 40(21Q22.3) MUTATED                                          1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                        7
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 40(21Q22.3) MUTATED                                                         1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                       1
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 40(21Q22.3) MUTATED                                            1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                          0
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 40(21Q22.3) MUTATED                                                  18
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                55
                                vv
clus                             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 40(21Q22.3) MUTATED                                                    0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                  3
                                vv
clus                             SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 40(21Q22.3) MUTATED                                    0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                  2
                                vv
clus                             SUPERFICIAL TRUNK - BACK
  DEL PEAK 40(21Q22.3) MUTATED                          2
  DEL PEAK 40(21Q22.3) WILD-TYPE                        3
                                vv
clus                             SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 40(21Q22.3) MUTATED                             2
  DEL PEAK 40(21Q22.3) WILD-TYPE                           2
                                vv
clus                             SUPERFICIAL TRUNK - FLANK
  DEL PEAK 40(21Q22.3) MUTATED                           0
  DEL PEAK 40(21Q22.3) WILD-TYPE                         1
                                vv
clus                             UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 40(21Q22.3) MUTATED                                   2
  DEL PEAK 40(21Q22.3) WILD-TYPE                                 5
                                vv
clus                             UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 40(21Q22.3) MUTATED                                   1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                 4
D65V3, multiclass
                                                         clus
vv                                                        DEL PEAK 40(21Q22.3) MUTATED
  CHEST - BREAST                                                                     0
  CHEST - CHEST WALL                                                                 2
  CHEST - LUNG/PLEURA                                                                0
  CHEST - MEDIASTINUM                                                                0
  CHEST - OTHER (PLEASE SPECIFY                                                      0
  GYNECOLOGICAL - OVARY                                                              0
  GYNECOLOGICAL - UTERUS                                                             6
  HEAD AND NECK - HEAD                                                               0
  HEAD AND NECK - NECK                                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                            0
  LOWER EXTREMITY - FOOT/ANKLE                                                       0
  LOWER EXTREMITY - GROIN                                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                                   9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                            1
  LOWER EXTREMITY - THIGH/KNEE                                                      15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                 18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                 0
  SUPERFICIAL TRUNK - BACK                                                           2
  SUPERFICIAL TRUNK - BUTTOCK                                                        2
  SUPERFICIAL TRUNK - FLANK                                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                  1
                                                         clus
vv                                                        DEL PEAK 40(21Q22.3) WILD-TYPE
  CHEST - BREAST                                                                       1
  CHEST - CHEST WALL                                                                   5
  CHEST - LUNG/PLEURA                                                                  2
  CHEST - MEDIASTINUM                                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                                        2
  GYNECOLOGICAL - OVARY                                                                1
  GYNECOLOGICAL - UTERUS                                                              22
  HEAD AND NECK - HEAD                                                                 2
  HEAD AND NECK - NECK                                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                      7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                              2
  LOWER EXTREMITY - FOOT/ANKLE                                                         4
  LOWER EXTREMITY - GROIN                                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                              4
  LOWER EXTREMITY - THIGH/KNEE                                                        29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                             7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                   55
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                   2
  SUPERFICIAL TRUNK - BACK                                                             3
  SUPERFICIAL TRUNK - BUTTOCK                                                          2
  SUPERFICIAL TRUNK - FLANK                                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                    4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                                cls
clus                               0   1
  DEL PEAK 40(21Q22.3) MUTATED    35  31
  DEL PEAK 40(21Q22.3) WILD-TYPE 104  87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED     35   31
  DEL PEAK 40(21Q22.3) WILD-TYPE  104   87
        clus
vv       DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  FEMALE                           35                            104
  MALE                             31                             87
[1] 2 2
[1] FALSE
D65V5, binary
                                cls
clus                               0   1
  DEL PEAK 40(21Q22.3) MUTATED    41  24
  DEL PEAK 40(21Q22.3) WILD-TYPE 138  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED     41   24
  DEL PEAK 40(21Q22.3) WILD-TYPE  138   48
     clus
vv    DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  NO                            41                            138
  YES                           24                             48
[1] 2 2
[1] FALSE
                                vv
clus                             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 40(21Q22.3) MUTATED                             16             0
  DEL PEAK 40(21Q22.3) WILD-TYPE                           43             2
                                vv
clus                             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 40(21Q22.3) MUTATED                                                                          0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                                        1
                                vv
clus                             LEIOMYOSARCOMA (LMS)
  DEL PEAK 40(21Q22.3) MUTATED                     20
  DEL PEAK 40(21Q22.3) WILD-TYPE                   83
                                vv
clus                             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 40(21Q22.3) MUTATED                                                  3
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                6
                                vv
clus                             MYXOFIBROSARCOMA
  DEL PEAK 40(21Q22.3) MUTATED                  5
  DEL PEAK 40(21Q22.3) WILD-TYPE               19
                                vv
clus                             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 40(21Q22.3) MUTATED                                                         14
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                       14
                                vv
clus                             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 40(21Q22.3) MUTATED                                          0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                        2
                                vv
clus                             SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 40(21Q22.3) MUTATED                             0
  DEL PEAK 40(21Q22.3) WILD-TYPE                           2
                                vv
clus                             SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 40(21Q22.3) MUTATED                               0
  DEL PEAK 40(21Q22.3) WILD-TYPE                             6
                                vv
clus                             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 40(21Q22.3) MUTATED                                            8
  DEL PEAK 40(21Q22.3) WILD-TYPE                                         13
D65V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 40(21Q22.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       16
  DESMOID TUMOR                                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                            0
  LEIOMYOSARCOMA (LMS)                                                                               20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                    3
  MYXOFIBROSARCOMA                                                                                    5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          8
                                                                          clus
vv                                                                         DEL PEAK 40(21Q22.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                         43
  DESMOID TUMOR                                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                              1
  LEIOMYOSARCOMA (LMS)                                                                                 83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                      6
  MYXOFIBROSARCOMA                                                                                     19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                             14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           13
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(21Q22.3) MUTATED    36  21   3   5
  DEL PEAK 40(21Q22.3) WILD-TYPE 116  48   6  21
D65V7, multiclass
    clus
vv   DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  R0                           36                            116
  R1                           21                             48
  R2                            3                              6
  RX                            5                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(21Q22.3) MUTATED       1                         4    60
  DEL PEAK 40(21Q22.3) WILD-TYPE     5                        14   164
D65V8, multiclass
                           clus
vv                          DEL PEAK 40(21Q22.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               60
                           clus
vv                          DEL PEAK 40(21Q22.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(21Q22.3) MUTATED     1  59
  DEL PEAK 40(21Q22.3) WILD-TYPE   4 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED      1   59
  DEL PEAK 40(21Q22.3) WILD-TYPE    4  161
                        clus
vv                       DEL PEAK 40(21Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 40(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 41(22Q13.32) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(22Q13.32) MUTATED    53  30
  DEL PEAK 41(22Q13.32) WILD-TYPE 106  68
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                             83                             174 
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                             30                              68 
$`DEL PEAK 41(22Q13.32) MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2H 
       16.18        67.20        34.36        15.22        14.43        15.85 
TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
      106.45       101.98        32.15        12.62        52.11        26.93 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-QQ-A8VB TCGA-3B-A9HI TCGA-3B-A9HR 
      159.29        22.62        11.70       188.15        50.01        88.57 
TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y 
       42.84        26.56        32.71        74.66        66.87         6.28 
TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 
        8.58         9.04       136.44        44.68        51.02        14.99 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YS 
       24.26        26.47        15.95        82.68        31.96        78.28 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       50.50        86.30        61.97        45.14        47.87        38.17 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-FX-A2QS 
      150.35        60.66        86.10        77.88        50.40        49.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5NA 
       21.70        20.32        19.89        34.88         4.57         9.80 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 
        3.22        19.89        25.22       171.09        13.58         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KD-A5QS 
       16.41         1.05         3.91       101.26         5.19        63.81 
TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-QC-AA9N TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-SG-A6Z4 
       16.41        25.41        17.65        64.77        10.52        18.94 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X2-A95T 
       22.82         8.61        19.63        13.41        84.79        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-Z4-AAPF 
       26.43        18.08        45.34        35.18        15.95 

$`DEL PEAK 41(22Q13.32) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BP 
       36.30        31.53        34.68        75.32        17.95        14.07 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       40.60        12.07        13.28        22.85        30.51        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-LI-A9QH 
       84.66        16.60        37.02        52.27        28.21        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS 
       41.49        35.08        19.69        53.49        68.55        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        14.37        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       18.64         0.56        14.04        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       18.54        54.21        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       76.41        27.81        60.30         9.70        95.38        79.17 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       49.05        86.83        33.44        31.86        35.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
        9.73        45.99        35.28        52.77        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       59.84        37.58        37.41        36.33        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       26.99         3.06        41.00        16.87        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
       48.20        20.05         9.34        40.77        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B 
       15.72        65.98        66.74         9.21       106.55        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N7 
       71.31        31.13        15.48         8.05        67.63        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IW-A3M4 
        0.72        80.48        19.53         1.38        37.12        85.97 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QU 
       53.33        62.17       123.78        17.36        23.38        35.28 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       30.31         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        13.08         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-RN-A68Q 
       48.59        35.90        37.12       130.32       111.98         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-A80G 
       16.77         3.88        25.35        32.75        13.22        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93         4.80        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
        8.58        35.90        30.84        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       29.46        27.32        36.43         4.37        13.38        15.98 

  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                           1.05                            0.49 
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                         188.15                          152.12 
  DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE 
                          26.93                           31.33 
[1] "1.1 - 188.2 (26.9)" "0.5 - 152.1 (31.3)"
[1] "hr=" "1.2"
D66V2, continuous
                                 vv
clus                              CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 41(22Q13.32) MUTATED                0                  2
  DEL PEAK 41(22Q13.32) WILD-TYPE              1                  5
                                 vv
clus                              CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 41(22Q13.32) MUTATED                     0                   0
  DEL PEAK 41(22Q13.32) WILD-TYPE                   2                   1
                                 vv
clus                              CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 41(22Q13.32) MUTATED                               1
  DEL PEAK 41(22Q13.32) WILD-TYPE                             1
                                 vv
clus                              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 41(22Q13.32) MUTATED                       1                     17
  DEL PEAK 41(22Q13.32) WILD-TYPE                     0                     11
                                 vv
clus                              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 41(22Q13.32) MUTATED                      0                    0
  DEL PEAK 41(22Q13.32) WILD-TYPE                    2                    1
                                 vv
clus                              HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 41(22Q13.32) MUTATED                                       0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                     2
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 41(22Q13.32) MUTATED                                  0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 41(22Q13.32) MUTATED                                                1
  DEL PEAK 41(22Q13.32) WILD-TYPE                                              1
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 41(22Q13.32) MUTATED                                 3
  DEL PEAK 41(22Q13.32) WILD-TYPE                               7
                                 vv
clus                              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 41(22Q13.32) MUTATED                                         0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                       2
                                 vv
clus                              LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 41(22Q13.32) MUTATED                              0
  DEL PEAK 41(22Q13.32) WILD-TYPE                            4
                                 vv
clus                              LOWER EXTREMITY - GROIN
  DEL PEAK 41(22Q13.32) MUTATED                         0
  DEL PEAK 41(22Q13.32) WILD-TYPE                       2
                                 vv
clus                              LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 41(22Q13.32) MUTATED                                  5
  DEL PEAK 41(22Q13.32) WILD-TYPE                               12
                                 vv
clus                              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 41(22Q13.32) MUTATED                                         2
  DEL PEAK 41(22Q13.32) WILD-TYPE                                       3
                                 vv
clus                              LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 41(22Q13.32) MUTATED                             19
  DEL PEAK 41(22Q13.32) WILD-TYPE                           25
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 41(22Q13.32) MUTATED                                         1
  DEL PEAK 41(22Q13.32) WILD-TYPE                                       3
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 41(22Q13.32) MUTATED                                           1
  DEL PEAK 41(22Q13.32) WILD-TYPE                                         1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 41(22Q13.32) MUTATED                                                  0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                5
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 41(22Q13.32) MUTATED                                          2
  DEL PEAK 41(22Q13.32) WILD-TYPE                                        6
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 41(22Q13.32) MUTATED                                                         1
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                       1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 41(22Q13.32) MUTATED                                            0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                          1
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 41(22Q13.32) MUTATED                                                  16
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                57
                                 vv
clus                              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 41(22Q13.32) MUTATED                                                    0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                  3
                                 vv
clus                              SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 41(22Q13.32) MUTATED                                    2
  DEL PEAK 41(22Q13.32) WILD-TYPE                                  0
                                 vv
clus                              SUPERFICIAL TRUNK - BACK
  DEL PEAK 41(22Q13.32) MUTATED                          1
  DEL PEAK 41(22Q13.32) WILD-TYPE                        4
                                 vv
clus                              SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 41(22Q13.32) MUTATED                             3
  DEL PEAK 41(22Q13.32) WILD-TYPE                           1
                                 vv
clus                              SUPERFICIAL TRUNK - FLANK
  DEL PEAK 41(22Q13.32) MUTATED                           0
  DEL PEAK 41(22Q13.32) WILD-TYPE                         1
                                 vv
clus                              UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 41(22Q13.32) MUTATED                                   3
  DEL PEAK 41(22Q13.32) WILD-TYPE                                 4
                                 vv
clus                              UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 41(22Q13.32) MUTATED                                   2
  DEL PEAK 41(22Q13.32) WILD-TYPE                                 3
D66V3, multiclass
                                                         clus
vv                                                        DEL PEAK 41(22Q13.32) MUTATED
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  2
  CHEST - LUNG/PLEURA                                                                 0
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       1
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             17
  HEAD AND NECK - HEAD                                                                0
  HEAD AND NECK - NECK                                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             0
  LOWER EXTREMITY - FOOT/ANKLE                                                        0
  LOWER EXTREMITY - GROIN                                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                                    5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            1
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
                                                         clus
vv                                                        DEL PEAK 41(22Q13.32) WILD-TYPE
  CHEST - BREAST                                                                        1
  CHEST - CHEST WALL                                                                    5
  CHEST - LUNG/PLEURA                                                                   2
  CHEST - MEDIASTINUM                                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                                         1
  GYNECOLOGICAL - OVARY                                                                 0
  GYNECOLOGICAL - UTERUS                                                               11
  HEAD AND NECK - HEAD                                                                  2
  HEAD AND NECK - NECK                                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                       7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                               2
  LOWER EXTREMITY - FOOT/ANKLE                                                          4
  LOWER EXTREMITY - GROIN                                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                                     12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                               3
  LOWER EXTREMITY - THIGH/KNEE                                                         25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                               3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                              6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                    57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                    0
  SUPERFICIAL TRUNK - BACK                                                              4
  SUPERFICIAL TRUNK - BUTTOCK                                                           1
  SUPERFICIAL TRUNK - FLANK                                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                     3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                                 cls
clus                               0  1
  DEL PEAK 41(22Q13.32) MUTATED   52 31
  DEL PEAK 41(22Q13.32) WILD-TYPE 87 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.32) MUTATED     52   31
  DEL PEAK 41(22Q13.32) WILD-TYPE   87   87
        clus
vv       DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE
  FEMALE                            52                              87
  MALE                              31                              87
[1] 2 2
[1] FALSE
D66V5, binary
                                 cls
clus                                0   1
  DEL PEAK 41(22Q13.32) MUTATED    56  25
  DEL PEAK 41(22Q13.32) WILD-TYPE 123  47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.32) MUTATED     56   25
  DEL PEAK 41(22Q13.32) WILD-TYPE  123   47
     clus
vv    DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE
  NO                             56                             123
  YES                            25                              47
[1] 2 2
[1] FALSE
                                 vv
clus                              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 41(22Q13.32) MUTATED                             14             0
  DEL PEAK 41(22Q13.32) WILD-TYPE                           45             2
                                 vv
clus                              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 41(22Q13.32) MUTATED                                                                          0
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                                        1
                                 vv
clus                              LEIOMYOSARCOMA (LMS)
  DEL PEAK 41(22Q13.32) MUTATED                     34
  DEL PEAK 41(22Q13.32) WILD-TYPE                   69
                                 vv
clus                              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 41(22Q13.32) MUTATED                                                  5
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                4
                                 vv
clus                              MYXOFIBROSARCOMA
  DEL PEAK 41(22Q13.32) MUTATED                  9
  DEL PEAK 41(22Q13.32) WILD-TYPE               15
                                 vv
clus                              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 41(22Q13.32) MUTATED                                                         11
  DEL PEAK 41(22Q13.32) WILD-TYPE                                                       17
                                 vv
clus                              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 41(22Q13.32) MUTATED                                          1
  DEL PEAK 41(22Q13.32) WILD-TYPE                                        1
                                 vv
clus                              SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 41(22Q13.32) MUTATED                             0
  DEL PEAK 41(22Q13.32) WILD-TYPE                           2
                                 vv
clus                              SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 41(22Q13.32) MUTATED                               0
  DEL PEAK 41(22Q13.32) WILD-TYPE                             6
                                 vv
clus                              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 41(22Q13.32) MUTATED                                            9
  DEL PEAK 41(22Q13.32) WILD-TYPE                                         12
D66V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 41(22Q13.32) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                        14
  DESMOID TUMOR                                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             0
  LEIOMYOSARCOMA (LMS)                                                                                34
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                     9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
                                                                          clus
vv                                                                         DEL PEAK 41(22Q13.32) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                          45
  DESMOID TUMOR                                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                               1
  LEIOMYOSARCOMA (LMS)                                                                                  69
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                       4
  MYXOFIBROSARCOMA                                                                                      15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                              17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                            12
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(22Q13.32) MUTATED    47  23   3  10
  DEL PEAK 41(22Q13.32) WILD-TYPE 105  46   6  16
D66V7, multiclass
    clus
vv   DEL PEAK 41(22Q13.32) MUTATED DEL PEAK 41(22Q13.32) WILD-TYPE
  R0                            47                             105
  R1                            23                              46
  R2                             3                               6
  RX                            10                              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(22Q13.32) MUTATED       2                         6    72
  DEL PEAK 41(22Q13.32) WILD-TYPE     4                        12   152
D66V8, multiclass
                           clus
vv                          DEL PEAK 41(22Q13.32) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                72
                           clus
vv                          DEL PEAK 41(22Q13.32) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                                 cls
clus                                0   1
  DEL PEAK 41(22Q13.32) MUTATED     1  69
  DEL PEAK 41(22Q13.32) WILD-TYPE   4 151
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.32) MUTATED      1   69
  DEL PEAK 41(22Q13.32) WILD-TYPE    4  151
                        clus
vv                       DEL PEAK 41(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            69
                        clus
vv                       DEL PEAK 41(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             151
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 42(XP21.1) MUTATION ANALYSIS
D67V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 42(XP21.1) MUTATED    31  24
  DEL PEAK 42(XP21.1) WILD-TYPE 128  74
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                           55                           202 
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                           24                            74 
$`DEL PEAK 42(XP21.1) MUTATED`
TCGA-DX-AB2W TCGA-DX-AB32 TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-LI-A9QH TCGA-QQ-A8VB 
      106.45       101.98        12.62        26.93        17.75       188.15 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L2 
       14.37        10.32        36.03        18.64         0.56        85.02 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48J 
        6.28         9.70         4.54        14.99        50.43         9.73 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BR TCGA-DX-AB2Q 
       37.41         3.06        16.87        21.30       150.35        66.74 
TCGA-DX-AB2T TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A48G TCGA-HS-A5NA TCGA-IF-A4AJ 
       77.88        71.31        49.15        19.89         9.80        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A42X TCGA-K1-A6RU TCGA-KD-A5QU 
      171.09        85.97         3.91       123.78        23.38        35.28 
TCGA-LI-A67I TCGA-MB-A8JL TCGA-PC-A5DO TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       30.31        19.73        81.01        18.94         3.88        22.82 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 
        8.61        19.63        65.46        63.35        18.08        50.86 
TCGA-Z4-AAPF 
       15.95 

$`DEL PEAK 42(XP21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       40.60        12.07        13.28        22.85        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IF-A4AK 
       84.66        32.15        16.60        37.02        52.11        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM 
       28.21       159.29        22.62        11.70         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       18.08        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-DX-A1KU 
       54.74        25.25        42.84        38.47        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       35.77        51.02        10.68        73.87        68.55        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BA 
       85.45        45.99        24.26        35.28        15.95        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       36.33        28.96        31.96        36.85        26.99        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       78.28        50.50        86.30        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A3RE 
        9.21       106.55        50.40        50.89        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       19.89        37.12        13.58         5.92        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS 
      101.26        53.33        62.17        17.36         5.19        63.81 
TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
       16.41        25.41         0.49        21.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        13.08        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT 
       10.52         0.72        16.77        25.35        32.75        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.41        10.72        12.46        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       38.27        22.62         8.58        26.43        35.90        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 
       30.84        35.18        19.17        20.65        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.98 

  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                         0.56                          0.49 
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE 
                        26.47                         31.91 
[1] "0.6 - 188.2 (26.5)" "0.5 - 159.3 (31.9)"
[1] "hr=" "1.1"
D67V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 42(XP21.1) MUTATED                1                  1
  DEL PEAK 42(XP21.1) WILD-TYPE              0                  6
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 42(XP21.1) MUTATED                     0                   0
  DEL PEAK 42(XP21.1) WILD-TYPE                   2                   1
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 42(XP21.1) MUTATED                               0
  DEL PEAK 42(XP21.1) WILD-TYPE                             2
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 42(XP21.1) MUTATED                       0                     12
  DEL PEAK 42(XP21.1) WILD-TYPE                     1                     16
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 42(XP21.1) MUTATED                      0                    0
  DEL PEAK 42(XP21.1) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 42(XP21.1) MUTATED                                       0
  DEL PEAK 42(XP21.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 42(XP21.1) MUTATED                                  0
  DEL PEAK 42(XP21.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 42(XP21.1) MUTATED                                                1
  DEL PEAK 42(XP21.1) WILD-TYPE                                              1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 42(XP21.1) MUTATED                                 0
  DEL PEAK 42(XP21.1) WILD-TYPE                              10
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 42(XP21.1) MUTATED                                         1
  DEL PEAK 42(XP21.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 42(XP21.1) MUTATED                              0
  DEL PEAK 42(XP21.1) WILD-TYPE                            4
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 42(XP21.1) MUTATED                         0
  DEL PEAK 42(XP21.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 42(XP21.1) MUTATED                                  3
  DEL PEAK 42(XP21.1) WILD-TYPE                               14
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 42(XP21.1) MUTATED                                         2
  DEL PEAK 42(XP21.1) WILD-TYPE                                       3
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 42(XP21.1) MUTATED                             12
  DEL PEAK 42(XP21.1) WILD-TYPE                           32
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 42(XP21.1) MUTATED                                         2
  DEL PEAK 42(XP21.1) WILD-TYPE                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 42(XP21.1) MUTATED                                           0
  DEL PEAK 42(XP21.1) WILD-TYPE                                         2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 42(XP21.1) MUTATED                                                  0
  DEL PEAK 42(XP21.1) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 42(XP21.1) MUTATED                                          3
  DEL PEAK 42(XP21.1) WILD-TYPE                                        5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 42(XP21.1) MUTATED                                                         1
  DEL PEAK 42(XP21.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 42(XP21.1) MUTATED                                            0
  DEL PEAK 42(XP21.1) WILD-TYPE                                          1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 42(XP21.1) MUTATED                                                  12
  DEL PEAK 42(XP21.1) WILD-TYPE                                                61
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 42(XP21.1) MUTATED                                                    2
  DEL PEAK 42(XP21.1) WILD-TYPE                                                  1
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 42(XP21.1) MUTATED                                    0
  DEL PEAK 42(XP21.1) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 42(XP21.1) MUTATED                          0
  DEL PEAK 42(XP21.1) WILD-TYPE                        5
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 42(XP21.1) MUTATED                             1
  DEL PEAK 42(XP21.1) WILD-TYPE                           3
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 42(XP21.1) MUTATED                           0
  DEL PEAK 42(XP21.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 42(XP21.1) MUTATED                                   0
  DEL PEAK 42(XP21.1) WILD-TYPE                                 7
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 42(XP21.1) MUTATED                                   1
  DEL PEAK 42(XP21.1) WILD-TYPE                                 4
D67V3, multiclass
                                                         clus
vv                                                        DEL PEAK 42(XP21.1) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                1
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               0
  CHEST - OTHER (PLEASE SPECIFY                                                     0
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           12
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      0
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           2
  LOWER EXTREMITY - THIGH/KNEE                                                     12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                                       1
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 1
                                                         clus
vv                                                        DEL PEAK 42(XP21.1) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  6
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                                       2
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             16
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      1
  LOWER ABDOMINAL/PELVIC - PELVIC                                                    10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        4
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                   14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             3
  LOWER EXTREMITY - THIGH/KNEE                                                       32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                                         3
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                               cls
clus                              0   1
  DEL PEAK 42(XP21.1) MUTATED    36  19
  DEL PEAK 42(XP21.1) WILD-TYPE 103  99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP21.1) MUTATED     36   19
  DEL PEAK 42(XP21.1) WILD-TYPE  103   99
        clus
vv       DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE
  FEMALE                          36                           103
  MALE                            19                            99
[1] 2 2
[1] FALSE
D67V5, binary
                               cls
clus                              0   1
  DEL PEAK 42(XP21.1) MUTATED    41  14
  DEL PEAK 42(XP21.1) WILD-TYPE 138  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP21.1) MUTATED     41   14
  DEL PEAK 42(XP21.1) WILD-TYPE  138   58
     clus
vv    DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE
  NO                           41                           138
  YES                          14                            58
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 42(XP21.1) MUTATED                              6             0
  DEL PEAK 42(XP21.1) WILD-TYPE                           53             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 42(XP21.1) MUTATED                                                                          0
  DEL PEAK 42(XP21.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 42(XP21.1) MUTATED                     31
  DEL PEAK 42(XP21.1) WILD-TYPE                   72
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 42(XP21.1) MUTATED                                                  3
  DEL PEAK 42(XP21.1) WILD-TYPE                                                6
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 42(XP21.1) MUTATED                  6
  DEL PEAK 42(XP21.1) WILD-TYPE               18
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 42(XP21.1) MUTATED                                                          6
  DEL PEAK 42(XP21.1) WILD-TYPE                                                       22
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 42(XP21.1) MUTATED                                          1
  DEL PEAK 42(XP21.1) WILD-TYPE                                        1
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 42(XP21.1) MUTATED                             0
  DEL PEAK 42(XP21.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 42(XP21.1) MUTATED                               1
  DEL PEAK 42(XP21.1) WILD-TYPE                             5
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 42(XP21.1) MUTATED                                            1
  DEL PEAK 42(XP21.1) WILD-TYPE                                         20
D67V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 42(XP21.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                       6
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              31
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   3
  MYXOFIBROSARCOMA                                                                                   6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                           6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           1
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                         1
                                                                          clus
vv                                                                         DEL PEAK 42(XP21.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        53
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                72
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     6
  MYXOFIBROSARCOMA                                                                                    18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            22
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                          20
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 42(XP21.1) MUTATED    33  11   3   8
  DEL PEAK 42(XP21.1) WILD-TYPE 119  58   6  18
D67V7, multiclass
    clus
vv   DEL PEAK 42(XP21.1) MUTATED DEL PEAK 42(XP21.1) WILD-TYPE
  R0                          33                           119
  R1                          11                            58
  R2                           3                             6
  RX                           8                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(XP21.1) MUTATED       0                         5    45
  DEL PEAK 42(XP21.1) WILD-TYPE     6                        13   179
D67V8, multiclass
                           clus
vv                          DEL PEAK 42(XP21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              45
                           clus
vv                          DEL PEAK 42(XP21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                               cls
clus                              0   1
  DEL PEAK 42(XP21.1) MUTATED     2  41
  DEL PEAK 42(XP21.1) WILD-TYPE   3 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP21.1) MUTATED      2   41
  DEL PEAK 42(XP21.1) WILD-TYPE    3  179
                        clus
vv                       DEL PEAK 42(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK 42(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           179
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 43(XQ21.1) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 43(XQ21.1) MUTATED   81 33
  DEL PEAK 43(XQ21.1) WILD-TYPE 78 65
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                          114                           143 
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                           33                            65 
$`DEL PEAK 43(XQ21.1) MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A8BG TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 
       31.53        67.20        17.95       106.45       101.98        30.51 
TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-QC-A6FX TCGA-QQ-A8VB 
       16.60        12.62        26.93        22.62        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       17.52        26.17        35.08        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23R 
       10.32        38.47        36.03        68.61        85.02        74.66 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U9 
       60.30         9.70       136.44        44.68        31.86        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A7EM TCGA-DX-A7EN 
       36.33         3.06        41.00        78.28        62.20        30.35 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-AB2F TCGA-DX-AB2T TCGA-DX-AB3C TCGA-FX-A2QS 
      150.35        27.95        12.00        77.88        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       21.70        19.89        67.63        34.88         4.57        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48         3.22         1.38        37.12        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
      171.09        85.97        16.41         3.91       101.26        62.17 
TCGA-K1-A42X TCGA-KD-A5QS TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H 
      123.78        63.81        30.31        25.41        19.73        14.99 
TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VC 
        7.36        38.63        81.01        17.65        18.08        35.90 
TCGA-QQ-A8VH TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
       10.52        22.82        19.63        13.41        10.72        12.46 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        38.27        65.46         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 
       18.08        30.84        35.18        20.65        50.86        27.32 

$`DEL PEAK 43(XQ21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        34.68        16.18        34.36        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X 
       14.43        14.07        15.85        40.60        12.07        13.28 
TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HS-A5N9 
       22.85        60.00        84.66        32.15        37.02        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.27        28.21       159.29        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
        6.35        18.08        41.49        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 
       68.55        88.57        44.91        54.74        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        32.71        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
        6.28        27.81         8.58        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       49.05        86.83        33.44        35.77        51.02         4.54 
TCGA-DX-A3UB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV 
       73.87        28.96        31.96        36.85        26.99        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BT TCGA-DX-A8BU 
      152.12        29.49        48.20        20.05        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
       60.66        19.43         6.58         1.15        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z 
       65.98        86.10        66.74         9.21       106.55        50.40 
TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HS-A5N8 
       50.89        31.13        20.32        15.48         8.05         0.72 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PO 
       19.53        19.89        13.58         5.92         1.05        53.33 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA 
       17.36        23.38         5.19        16.41        35.28         0.49 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK 
       21.73        17.98        22.39        11.57        10.45       122.96 
TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD 
       37.55        13.08         1.84        46.82        48.59        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32       111.98        64.77         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO 
        3.88        25.35        32.75         8.61        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C7 
        4.80        22.62        26.43        45.34        19.17        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                         1.38                          0.49 
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE 
                        35.13                         26.99 
[1] "1.4 - 188.2 (35.1)" "0.5 - 159.3 (27.0)"
[1] "hr=" "1.9"
D68V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 43(XQ21.1) MUTATED                1                  3
  DEL PEAK 43(XQ21.1) WILD-TYPE              0                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 43(XQ21.1) MUTATED                     0                   1
  DEL PEAK 43(XQ21.1) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 43(XQ21.1) MUTATED                               2
  DEL PEAK 43(XQ21.1) WILD-TYPE                             0
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 43(XQ21.1) MUTATED                       1                     16
  DEL PEAK 43(XQ21.1) WILD-TYPE                     0                     12
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 43(XQ21.1) MUTATED                      0                    0
  DEL PEAK 43(XQ21.1) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 43(XQ21.1) MUTATED                                       0
  DEL PEAK 43(XQ21.1) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 43(XQ21.1) MUTATED                                  0
  DEL PEAK 43(XQ21.1) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 43(XQ21.1) MUTATED                                                2
  DEL PEAK 43(XQ21.1) WILD-TYPE                                              0
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 43(XQ21.1) MUTATED                                 4
  DEL PEAK 43(XQ21.1) WILD-TYPE                               6
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 43(XQ21.1) MUTATED                                         1
  DEL PEAK 43(XQ21.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 43(XQ21.1) MUTATED                              1
  DEL PEAK 43(XQ21.1) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 43(XQ21.1) MUTATED                         0
  DEL PEAK 43(XQ21.1) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 43(XQ21.1) MUTATED                                  9
  DEL PEAK 43(XQ21.1) WILD-TYPE                                8
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 43(XQ21.1) MUTATED                                         4
  DEL PEAK 43(XQ21.1) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 43(XQ21.1) MUTATED                             18
  DEL PEAK 43(XQ21.1) WILD-TYPE                           26
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 43(XQ21.1) MUTATED                                         3
  DEL PEAK 43(XQ21.1) WILD-TYPE                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 43(XQ21.1) MUTATED                                           2
  DEL PEAK 43(XQ21.1) WILD-TYPE                                         0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 43(XQ21.1) MUTATED                                                  1
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 43(XQ21.1) MUTATED                                          4
  DEL PEAK 43(XQ21.1) WILD-TYPE                                        4
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 43(XQ21.1) MUTATED                                                         1
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 43(XQ21.1) MUTATED                                            1
  DEL PEAK 43(XQ21.1) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 43(XQ21.1) MUTATED                                                  27
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                46
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 43(XQ21.1) MUTATED                                                    2
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                  1
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 43(XQ21.1) MUTATED                                    0
  DEL PEAK 43(XQ21.1) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 43(XQ21.1) MUTATED                          2
  DEL PEAK 43(XQ21.1) WILD-TYPE                        3
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 43(XQ21.1) MUTATED                             2
  DEL PEAK 43(XQ21.1) WILD-TYPE                           2
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 43(XQ21.1) MUTATED                           0
  DEL PEAK 43(XQ21.1) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 43(XQ21.1) MUTATED                                   4
  DEL PEAK 43(XQ21.1) WILD-TYPE                                 3
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 43(XQ21.1) MUTATED                                   2
  DEL PEAK 43(XQ21.1) WILD-TYPE                                 3
D68V3, multiclass
                                                         clus
vv                                                        DEL PEAK 43(XQ21.1) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             1
  GYNECOLOGICAL - UTERUS                                                           16
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                  9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           4
  LOWER EXTREMITY - THIGH/KNEE                                                     18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          2
  SUPERFICIAL TRUNK - BUTTOCK                                                       2
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 2
                                                         clus
vv                                                        DEL PEAK 43(XQ21.1) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       0
  GYNECOLOGICAL - OVARY                                                               0
  GYNECOLOGICAL - UTERUS                                                             12
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             1
  LOWER EXTREMITY - THIGH/KNEE                                                       26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            3
  SUPERFICIAL TRUNK - BUTTOCK                                                         2
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   3
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                               cls
clus                             0  1
  DEL PEAK 43(XQ21.1) MUTATED   71 43
  DEL PEAK 43(XQ21.1) WILD-TYPE 68 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XQ21.1) MUTATED     71   43
  DEL PEAK 43(XQ21.1) WILD-TYPE   68   75
        clus
vv       DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE
  FEMALE                          71                            68
  MALE                            43                            75
[1] 2 2
[1] FALSE
D68V5, binary
                               cls
clus                              0   1
  DEL PEAK 43(XQ21.1) MUTATED    79  33
  DEL PEAK 43(XQ21.1) WILD-TYPE 100  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XQ21.1) MUTATED     79   33
  DEL PEAK 43(XQ21.1) WILD-TYPE  100   39
     clus
vv    DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE
  NO                           79                           100
  YES                          33                            39
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 43(XQ21.1) MUTATED                             16             0
  DEL PEAK 43(XQ21.1) WILD-TYPE                           43             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 43(XQ21.1) MUTATED                                                                          0
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 43(XQ21.1) MUTATED                     62
  DEL PEAK 43(XQ21.1) WILD-TYPE                   41
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 43(XQ21.1) MUTATED                                                  4
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                5
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 43(XQ21.1) MUTATED                  9
  DEL PEAK 43(XQ21.1) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 43(XQ21.1) MUTATED                                                         10
  DEL PEAK 43(XQ21.1) WILD-TYPE                                                       18
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 43(XQ21.1) MUTATED                                          0
  DEL PEAK 43(XQ21.1) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 43(XQ21.1) MUTATED                             0
  DEL PEAK 43(XQ21.1) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 43(XQ21.1) MUTATED                               1
  DEL PEAK 43(XQ21.1) WILD-TYPE                             5
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 43(XQ21.1) MUTATED                                           12
  DEL PEAK 43(XQ21.1) WILD-TYPE                                          9
D68V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 43(XQ21.1) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      16
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              62
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   4
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        12
                                                                          clus
vv                                                                         DEL PEAK 43(XQ21.1) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        43
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                41
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 43(XQ21.1) MUTATED   73 26  2 13
  DEL PEAK 43(XQ21.1) WILD-TYPE 79 43  7 13
D68V7, multiclass
    clus
vv   DEL PEAK 43(XQ21.1) MUTATED DEL PEAK 43(XQ21.1) WILD-TYPE
  R0                          73                            79
  R1                          26                            43
  R2                           2                             7
  RX                          13                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(XQ21.1) MUTATED       2                        11    98
  DEL PEAK 43(XQ21.1) WILD-TYPE     4                         7   126
D68V8, multiclass
                           clus
vv                          DEL PEAK 43(XQ21.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              98
                           clus
vv                          DEL PEAK 43(XQ21.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                               cls
clus                              0   1
  DEL PEAK 43(XQ21.1) MUTATED     1 101
  DEL PEAK 43(XQ21.1) WILD-TYPE   4 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XQ21.1) MUTATED      1  101
  DEL PEAK 43(XQ21.1) WILD-TYPE    4  119
                        clus
vv                       DEL PEAK 43(XQ21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         101
                        clus
vv                       DEL PEAK 43(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           119
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 44(XQ22.3) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 44(XQ22.3) MUTATED   85 38
  DEL PEAK 44(XQ22.3) WILD-TYPE 74 60
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                          123                           134 
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                           38                            60 
$`DEL PEAK 44(XQ22.3) MUTATED`
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X 
       67.20        34.36        17.95        15.85       106.45        13.28 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
      101.98        30.51        37.02        12.62        52.11        26.93 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB 
       28.21        22.62        17.75         6.35        18.08       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HU 
       17.52        26.17        35.08        50.01        19.69        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KX 
       42.84        10.32        38.47        36.03        26.56        68.61 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LW 
       12.85        18.54        85.02        60.30         9.70       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD 
       33.44        44.68        14.99        10.68        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88        85.45         9.73        24.26        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM 
       82.68        36.33        78.28        86.30        64.21        62.20 
TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       30.35         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS 
       40.77       150.35        40.44        36.69         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB3C TCGA-FX-A3TO 
       12.00        86.10        66.74        77.88        71.31        20.32 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       19.89        67.63        34.88        33.30         9.80        80.48 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
       19.89        37.12        25.22       171.09        13.58        85.97 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS 
       16.41       101.26        62.17       123.78         5.19        63.81 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DN TCGA-QC-AA9N 
       35.28        25.41        19.73        14.99        38.63        17.65 
TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       35.90        10.52        16.77        19.63        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
       12.46        84.79        38.27        65.46         8.58        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 
       35.90        18.08        45.34        30.84        35.18        20.65 
TCGA-X6-A8C5 TCGA-X9-A971 TCGA-X9-A973 
       50.86        27.32        36.43 

$`DEL PEAK 44(XQ22.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        16.18        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB36 
       14.43        14.07        40.60        12.07        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-KF-A41W 
       84.66        32.15        16.60        52.27       159.29        11.70 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
        8.28        20.94        41.49        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       44.91        54.74        14.37        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       32.71        45.11        54.21        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ 
        5.26        76.41        66.87         6.28        27.81         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U5 
       95.38        79.17         9.04        49.05        86.83        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48N 
       35.77        51.02         4.54        73.87        45.99        35.28 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO 
       50.50        16.87       101.23        21.30        34.49       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX 
       29.49        48.20        20.05        27.95        60.66        19.43 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z 
       17.79        15.72        65.98         9.21       106.55        50.40 
TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO 
       50.89        49.15        31.13        21.70        15.48         8.05 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IW-A3M5 
        4.57         0.72        19.53         3.22         1.38         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT 
        1.05         3.91        53.33        17.36        23.38        16.41 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       30.31         0.49        21.73        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 
       10.45         7.36       122.96        37.55        81.01        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        46.82        18.08        48.59        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
      111.98        64.77         0.72        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       25.35        32.75         8.61        13.22        11.93         4.80 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       22.62        26.43        19.17        29.46         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                         1.15                          0.49 
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                       188.15                        159.29 
  DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE 
                        35.28                         26.71 
[1] "1.1 - 188.2 (35.3)" "0.5 - 159.3 (26.7)"
[1] "hr=" "1.8"
D69V2, continuous
                               vv
clus                            CHEST - BREAST CHEST - CHEST WALL
  DEL PEAK 44(XQ22.3) MUTATED                1                  3
  DEL PEAK 44(XQ22.3) WILD-TYPE              0                  4
                               vv
clus                            CHEST - LUNG/PLEURA CHEST - MEDIASTINUM
  DEL PEAK 44(XQ22.3) MUTATED                     0                   1
  DEL PEAK 44(XQ22.3) WILD-TYPE                   2                   0
                               vv
clus                            CHEST - OTHER (PLEASE SPECIFY
  DEL PEAK 44(XQ22.3) MUTATED                               2
  DEL PEAK 44(XQ22.3) WILD-TYPE                             0
                               vv
clus                            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  DEL PEAK 44(XQ22.3) MUTATED                       0                     18
  DEL PEAK 44(XQ22.3) WILD-TYPE                     1                     10
                               vv
clus                            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  DEL PEAK 44(XQ22.3) MUTATED                      0                    0
  DEL PEAK 44(XQ22.3) WILD-TYPE                    2                    1
                               vv
clus                            HEAD AND NECK - OTHER (PLEASE SPECIFY
  DEL PEAK 44(XQ22.3) MUTATED                                       0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                     2
                               vv
clus                            LOWER ABDOMINAL/PELVIC - BLADDER
  DEL PEAK 44(XQ22.3) MUTATED                                  0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                1
                               vv
clus                            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  DEL PEAK 44(XQ22.3) MUTATED                                                2
  DEL PEAK 44(XQ22.3) WILD-TYPE                                              0
                               vv
clus                            LOWER ABDOMINAL/PELVIC - PELVIC
  DEL PEAK 44(XQ22.3) MUTATED                                 5
  DEL PEAK 44(XQ22.3) WILD-TYPE                               5
                               vv
clus                            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  DEL PEAK 44(XQ22.3) MUTATED                                         1
  DEL PEAK 44(XQ22.3) WILD-TYPE                                       1
                               vv
clus                            LOWER EXTREMITY - FOOT/ANKLE
  DEL PEAK 44(XQ22.3) MUTATED                              1
  DEL PEAK 44(XQ22.3) WILD-TYPE                            3
                               vv
clus                            LOWER EXTREMITY - GROIN
  DEL PEAK 44(XQ22.3) MUTATED                         0
  DEL PEAK 44(XQ22.3) WILD-TYPE                       2
                               vv
clus                            LOWER EXTREMITY - LOWER LEG/CALF
  DEL PEAK 44(XQ22.3) MUTATED                                 12
  DEL PEAK 44(XQ22.3) WILD-TYPE                                5
                               vv
clus                            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  DEL PEAK 44(XQ22.3) MUTATED                                         3
  DEL PEAK 44(XQ22.3) WILD-TYPE                                       2
                               vv
clus                            LOWER EXTREMITY - THIGH/KNEE
  DEL PEAK 44(XQ22.3) MUTATED                             20
  DEL PEAK 44(XQ22.3) WILD-TYPE                           24
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  DEL PEAK 44(XQ22.3) MUTATED                                         3
  DEL PEAK 44(XQ22.3) WILD-TYPE                                       1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  DEL PEAK 44(XQ22.3) MUTATED                                           1
  DEL PEAK 44(XQ22.3) WILD-TYPE                                         1
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  DEL PEAK 44(XQ22.3) MUTATED                                                  0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                5
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  DEL PEAK 44(XQ22.3) MUTATED                                          2
  DEL PEAK 44(XQ22.3) WILD-TYPE                                        6
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  DEL PEAK 44(XQ22.3) MUTATED                                                         0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                       2
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  DEL PEAK 44(XQ22.3) MUTATED                                            1
  DEL PEAK 44(XQ22.3) WILD-TYPE                                          0
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  DEL PEAK 44(XQ22.3) MUTATED                                                  31
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                42
                               vv
clus                            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  DEL PEAK 44(XQ22.3) MUTATED                                                    2
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                  1
                               vv
clus                            SUPERFICIAL TRUNK - ABDOMINAL WALL
  DEL PEAK 44(XQ22.3) MUTATED                                    0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                  2
                               vv
clus                            SUPERFICIAL TRUNK - BACK
  DEL PEAK 44(XQ22.3) MUTATED                          1
  DEL PEAK 44(XQ22.3) WILD-TYPE                        4
                               vv
clus                            SUPERFICIAL TRUNK - BUTTOCK
  DEL PEAK 44(XQ22.3) MUTATED                             4
  DEL PEAK 44(XQ22.3) WILD-TYPE                           0
                               vv
clus                            SUPERFICIAL TRUNK - FLANK
  DEL PEAK 44(XQ22.3) MUTATED                           0
  DEL PEAK 44(XQ22.3) WILD-TYPE                         1
                               vv
clus                            UPPER EXTREMITY - SHOULDER/AXILLA
  DEL PEAK 44(XQ22.3) MUTATED                                   6
  DEL PEAK 44(XQ22.3) WILD-TYPE                                 1
                               vv
clus                            UPPER EXTREMITY - UPPER ARM/ELBOW
  DEL PEAK 44(XQ22.3) MUTATED                                   3
  DEL PEAK 44(XQ22.3) WILD-TYPE                                 2
D69V3, multiclass
                                                         clus
vv                                                        DEL PEAK 44(XQ22.3) MUTATED
  CHEST - BREAST                                                                    1
  CHEST - CHEST WALL                                                                3
  CHEST - LUNG/PLEURA                                                               0
  CHEST - MEDIASTINUM                                                               1
  CHEST - OTHER (PLEASE SPECIFY                                                     2
  GYNECOLOGICAL - OVARY                                                             0
  GYNECOLOGICAL - UTERUS                                                           18
  HEAD AND NECK - HEAD                                                              0
  HEAD AND NECK - NECK                                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - PELVIC                                                   5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                           1
  LOWER EXTREMITY - FOOT/ANKLE                                                      1
  LOWER EXTREMITY - GROIN                                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                                 12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                           3
  LOWER EXTREMITY - THIGH/KNEE                                                     20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                           3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                         1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                  0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                          2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                31
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                0
  SUPERFICIAL TRUNK - BACK                                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                                       4
  SUPERFICIAL TRUNK - FLANK                                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                                 6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                 3
                                                         clus
vv                                                        DEL PEAK 44(XQ22.3) WILD-TYPE
  CHEST - BREAST                                                                      0
  CHEST - CHEST WALL                                                                  4
  CHEST - LUNG/PLEURA                                                                 2
  CHEST - MEDIASTINUM                                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                                       0
  GYNECOLOGICAL - OVARY                                                               1
  GYNECOLOGICAL - UTERUS                                                             10
  HEAD AND NECK - HEAD                                                                2
  HEAD AND NECK - NECK                                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                                     5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                             1
  LOWER EXTREMITY - FOOT/ANKLE                                                        3
  LOWER EXTREMITY - GROIN                                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                                    5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                             2
  LOWER EXTREMITY - THIGH/KNEE                                                       24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                             1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                            6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                                  42
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                                  2
  SUPERFICIAL TRUNK - BACK                                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                                         0
  SUPERFICIAL TRUNK - FLANK                                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                                   1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                                   2
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                               cls
clus                             0  1
  DEL PEAK 44(XQ22.3) MUTATED   75 48
  DEL PEAK 44(XQ22.3) WILD-TYPE 64 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 44(XQ22.3) MUTATED     75   48
  DEL PEAK 44(XQ22.3) WILD-TYPE   64   70
        clus
vv       DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE
  FEMALE                          75                            64
  MALE                            48                            70
[1] 2 2
[1] FALSE
D69V5, binary
                               cls
clus                             0  1
  DEL PEAK 44(XQ22.3) MUTATED   83 39
  DEL PEAK 44(XQ22.3) WILD-TYPE 96 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 44(XQ22.3) MUTATED     83   39
  DEL PEAK 44(XQ22.3) WILD-TYPE   96   33
     clus
vv    DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE
  NO                           83                            96
  YES                          39                            33
[1] 2 2
[1] FALSE
                               vv
clus                            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  DEL PEAK 44(XQ22.3) MUTATED                             15             0
  DEL PEAK 44(XQ22.3) WILD-TYPE                           44             2
                               vv
clus                            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  DEL PEAK 44(XQ22.3) MUTATED                                                                          0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                                        1
                               vv
clus                            LEIOMYOSARCOMA (LMS)
  DEL PEAK 44(XQ22.3) MUTATED                     66
  DEL PEAK 44(XQ22.3) WILD-TYPE                   37
                               vv
clus                            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  DEL PEAK 44(XQ22.3) MUTATED                                                  4
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                5
                               vv
clus                            MYXOFIBROSARCOMA
  DEL PEAK 44(XQ22.3) MUTATED                  9
  DEL PEAK 44(XQ22.3) WILD-TYPE               15
                               vv
clus                            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  DEL PEAK 44(XQ22.3) MUTATED                                                         15
  DEL PEAK 44(XQ22.3) WILD-TYPE                                                       13
                               vv
clus                            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  DEL PEAK 44(XQ22.3) MUTATED                                          0
  DEL PEAK 44(XQ22.3) WILD-TYPE                                        2
                               vv
clus                            SYNOVIAL SARCOMA - BIPHASIC
  DEL PEAK 44(XQ22.3) MUTATED                             0
  DEL PEAK 44(XQ22.3) WILD-TYPE                           2
                               vv
clus                            SYNOVIAL SARCOMA - MONOPHASIC
  DEL PEAK 44(XQ22.3) MUTATED                               1
  DEL PEAK 44(XQ22.3) WILD-TYPE                             5
                               vv
clus                            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  DEL PEAK 44(XQ22.3) MUTATED                                           13
  DEL PEAK 44(XQ22.3) WILD-TYPE                                          8
D69V6, multiclass
                                                                          clus
vv                                                                         DEL PEAK 44(XQ22.3) MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                                      15
  DESMOID TUMOR                                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                           0
  LEIOMYOSARCOMA (LMS)                                                                              66
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                   4
  MYXOFIBROSARCOMA                                                                                   9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                          15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                        13
                                                                          clus
vv                                                                         DEL PEAK 44(XQ22.3) WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                                        44
  DESMOID TUMOR                                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                             1
  LEIOMYOSARCOMA (LMS)                                                                                37
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                                     5
  MYXOFIBROSARCOMA                                                                                    15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                            13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                           8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 44(XQ22.3) MUTATED   81 31  3  7
  DEL PEAK 44(XQ22.3) WILD-TYPE 71 38  6 19
D69V7, multiclass
    clus
vv   DEL PEAK 44(XQ22.3) MUTATED DEL PEAK 44(XQ22.3) WILD-TYPE
  R0                          81                            71
  R1                          31                            38
  R2                           3                             6
  RX                           7                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(XQ22.3) MUTATED       2                        10   108
  DEL PEAK 44(XQ22.3) WILD-TYPE     4                         8   116
D69V8, multiclass
                           clus
vv                          DEL PEAK 44(XQ22.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             108
                           clus
vv                          DEL PEAK 44(XQ22.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                               cls
clus                              0   1
  DEL PEAK 44(XQ22.3) MUTATED     1 106
  DEL PEAK 44(XQ22.3) WILD-TYPE   4 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 44(XQ22.3) MUTATED      1  106
  DEL PEAK 44(XQ22.3) WILD-TYPE    4  114
                        clus
vv                       DEL PEAK 44(XQ22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       DEL PEAK 44(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           114
[1] 2 2
[1] FALSE
