[1] "ofn"        "-oTESCA-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/ESCA-TP/22506419/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22519066/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=184, common to both=184
[1]  82 184
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           40                           144 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           40                           144 
[1] "AMP PEAK  2(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           93                            91 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           93                            91 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           96                            88 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           96                            88 
[1] "AMP PEAK  4(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           60                           124 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           60                           124 
[1] "AMP PEAK  5(2Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           60                           124 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           60                           124 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          128                            56 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          128                            56 
[1] "AMP PEAK  7(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           36                           148 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           36                           148 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            98                             86 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            98                             86 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           69                           115 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           69                           115 
[1] "AMP PEAK 10(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           42                           142 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           42                           142 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          125                            59 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          125                            59 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          114                            70 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          114                            70 
[1] "AMP PEAK 13(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           52                           132 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           52                           132 
[1] "AMP PEAK 14(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            86                             98 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            86                             98 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           145                             39 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           145                             39 
[1] "AMP PEAK 16(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           40                           144 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           40                           144 
[1] "AMP PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           64                           120 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           64                           120 
[1] "AMP PEAK 18(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          52                          132 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          52                          132 
[1] "AMP PEAK 19(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          50                          134 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          50                          134 
[1] "AMP PEAK 20(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           104                             80 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           104                             80 
[1] "AMP PEAK 21(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            79                            105 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            79                            105 
[1] "AMP PEAK 22(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          51                          133 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          51                          133 
[1] "AMP PEAK 23(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            65                            119 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            65                            119 
[1] "AMP PEAK 24(14Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            61                            123 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            61                            123 
[1] "AMP PEAK 25(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            58                            126 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            58                            126 
[1] "AMP PEAK 26(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          75                          109 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          75                          109 
[1] "AMP PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             69                             115 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             69                             115 
[1] "AMP PEAK 28(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            59                            125 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            59                            125 
[1] "AMP PEAK 29(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          55                          129 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          55                          129 
[1] "AMP PEAK 30(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         69                         115 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         69                         115 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            75                            109 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            75                            109 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           64                           120 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           64                           120 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         167 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         167 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           59                           125 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           59                           125 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           36                           148 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           36                           148 
[1] "DEL PEAK  6(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          111                            73 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          111                            73 
[1] "DEL PEAK  7(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          126                            58 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          126                            58 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          125                            59 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          125                            59 
[1] "DEL PEAK  9(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           33                           151 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           33                           151 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            16                            168 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            16                            168 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          106                            78 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          106                            78 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          105                            79 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          105                            79 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           99                            85 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           99                            85 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          112                            72 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          112                            72 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           74                           110 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           74                           110 
[1] "DEL PEAK 16(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           55                           129 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           55                           129 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         50                         134 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         50                         134 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           56                           128 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           56                           128 
[1] "DEL PEAK 19(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           67                           117 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           67                           117 
[1] "DEL PEAK 20(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           92                            92 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           92                            92 
[1] "DEL PEAK 21(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         75                         109 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         75                         109 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        108                          76 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        108                          76 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          141                            43 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          141                            43 
[1] "DEL PEAK 24(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            54                            130 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            54                            130 
[1] "DEL PEAK 25(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             52                             132 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             52                             132 
[1] "DEL PEAK 26(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            46                            138 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            46                            138 
[1] "DEL PEAK 27(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             65                             119 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             65                             119 
[1] "DEL PEAK 28(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            79                            105 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            79                            105 
[1] "DEL PEAK 29(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          81                          103 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          81                          103 
[1] "DEL PEAK 30(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            52                            132 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            52                            132 
[1] "DEL PEAK 31(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             76                             108 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             76                             108 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            74                            110 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            74                            110 
[1] "DEL PEAK 33(13Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             69                             115 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             69                             115 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            51                            133 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            51                            133 
[1] "DEL PEAK 35(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            63                            121 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            63                            121 
[1] "DEL PEAK 36(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            65                            119 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            65                            119 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            84                            100 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            84                            100 
[1] "DEL PEAK 38(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          86                           98 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          86                           98 
[1] "DEL PEAK 39(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            41                            143 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            41                            143 
[1] "DEL PEAK 40(18P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             60                             124 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             60                             124 
[1] "DEL PEAK 41(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           111                             73 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           111                             73 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           119                             65 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           119                             65 
[1] "DEL PEAK 43(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           112                             72 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           112                             72 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            94                             90 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            94                             90 
[1] "DEL PEAK 45(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            33                            151 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            33                            151 
[1] "DEL PEAK 46(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                           107                             77 
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                           107                             77 
[1] "DEL PEAK 47(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                            108                              76 
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                            108                              76 
[1] "DEL PEAK 48(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                            79                            105 
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                            79                            105 
[1] "DEL PEAK 49(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           70                           114 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           70                           114 
[1] "DEL PEAK 50(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                           75                           109 
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                           75                           109 
[1] "DEL PEAK 51(XQ11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                           43                           141 
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                           43                           141 
[1] "DEL PEAK 52(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            41                            143 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            41                            143 
[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] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 184 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=74,	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=96,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'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] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 184 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "NUMBER_PACK_YEARS_SMOKED"   
[11] "RESIDUAL_TUMOR"              "NUMBER_OF_LYMPH_NODES"      
[13] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 31 43 87  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   32    43    87     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 31 43 87  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   32    43    87     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
77 68 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
77 68 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
77 68 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
77 68 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=46, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=14, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P34.2) MUTATED   22 18
  AMP PEAK  1(1P34.2) WILD-TYPE 86 58
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           40                           144 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           18                            58 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-L5-A88Y TCGA-2H-A9GN TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.36         8.94        20.78        17.03         4.67       122.10 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW 
       47.38        25.22        47.93        18.35         1.38         7.13 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS 
        3.75         3.02        55.50         2.66        13.22        13.41 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A9 
       10.85        10.45        13.15        13.25        12.62        11.54 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6XQ 
       12.03         0.13        12.03         8.02        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EX 
       53.95        12.69         3.42        27.09        22.82        28.11 
TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24        25.08         2.10        19.73 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        21.01         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        7.40        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.38        15.35        12.59        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ 
       12.23        13.18        12.33        13.38        13.18        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       25.81        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        41.23        14.37         3.42         1.32         2.66 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.13                          0.30 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       12.655                        13.180 
[1] "0.1 - 122.1 (12.7)" "0.3 - 83.2 (13.2)" 
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P34.2) MUTATED         2        1        0        0         6
  AMP PEAK  1(1P34.2) WILD-TYPE       6        4        6        1        41
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P34.2) MUTATED           7         5          4          2
  AMP PEAK  1(1P34.2) WILD-TYPE        24        20         10          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P34.2) MUTATED            1        1         2
  AMP PEAK  1(1P34.2) WILD-TYPE          6        4         2
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                            6                            41
  STAGE IIB                            7                            24
  STAGE III                            5                            20
  STAGE IIIA                           4                            10
  STAGE IIIB                           2                             7
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  1(1P34.2) MUTATED       8  9 15  1
  AMP PEAK  1(1P34.2) WILD-TYPE    24 34 72  4
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1                           8                            24
  T2                              9                            34
  T3                             15                            72
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  1(1P34.2) MUTATED   13 15  3  2
  AMP PEAK  1(1P34.2) WILD-TYPE 64 53  9  6
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          13                            64
  N1                          15                            53
  N2                           3                             9
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    25   3
  AMP PEAK  1(1P34.2) WILD-TYPE 110   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     25    3
  AMP PEAK  1(1P34.2) WILD-TYPE  110    6
   clus
vv  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  0                          25                           110
  1                           3                             6
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     5  35
  AMP PEAK  1(1P34.2) WILD-TYPE  22 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      5   35
  AMP PEAK  1(1P34.2) WILD-TYPE   22  122
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           5                            22
  MALE                            35                           122
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED   25  9
  AMP PEAK  1(1P34.2) WILD-TYPE 98 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     25    9
  AMP PEAK  1(1P34.2) WILD-TYPE   98   34
     clus
vv    AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  NO                           25                            98
  YES                           9                            34
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED   21 19
  AMP PEAK  1(1P34.2) WILD-TYPE 67 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     21   19
  AMP PEAK  1(1P34.2) WILD-TYPE   67   77
                                   clus
vv                                  AMP PEAK  1(1P34.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              21
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          19
                                   clus
vv                                  AMP PEAK  1(1P34.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            77
[1] 2 2
[1] FALSE
D1V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P34.2) MUTATED    30   0   0   2
  AMP PEAK  1(1P34.2) WILD-TYPE 107  12   2   5
D1V12, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  R0                          30                           107
  R1                           0                            12
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       9                         3    25
  AMP PEAK  1(1P34.2) WILD-TYPE    37                         2    89
D1V14, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              25
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                37
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    2 18
  AMP PEAK  1(1P34.2) WILD-TYPE  4 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      2   18
  AMP PEAK  1(1P34.2) WILD-TYPE    4   70
                        clus
vv                       AMP PEAK  1(1P34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK  1(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            70
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q23.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q23.3) MUTATED   53 40
  AMP PEAK  2(1Q23.3) WILD-TYPE 55 36
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           93                            91 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           40                            36 
$`AMP PEAK  2(1Q23.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OI TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ 
       60.39        19.99         0.36        20.02        31.27        58.55 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
       13.94         8.94        16.24         4.21         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.79        23.41        12.82         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH 
       44.75         3.68        31.56        25.22         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT 
       21.01        47.93        18.35         7.17         1.38         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         2.60         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
        2.66        12.92        16.47        13.22         5.49        13.41 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S 
       52.57        10.85         5.92        10.45        12.66        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       15.35        12.59        12.49        12.76        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.22         4.47        12.33        12.00        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        8.02        16.31        38.40         6.35        53.95        15.78 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EQ 
       12.69        20.38         3.42        16.44        25.81        22.82 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE 
        8.12        28.11        18.21        25.08        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

$`AMP PEAK  2(1Q23.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF 
        4.70        22.82        35.97        27.12         5.16        25.78 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YA 
       14.30         7.63         5.92        32.45        33.27        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FD 
        2.63         9.30         9.96        14.86        12.16        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        47.38        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS 
        3.16        30.25        26.33         3.32         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NI TCGA-L5-A8NK 
       29.00         7.13        15.48        25.12        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        7.76        21.37         8.71        83.24        46.09        10.36 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X 
       12.43        13.41        12.33        13.38        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.59        12.59        22.39        12.85        15.52 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FW 
       25.25        10.52        12.23        12.03        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59         5.06         7.04         9.30         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        7.00         5.29        15.35         9.27         8.98        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55        18.31        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       46.19        18.05        11.24         9.17        15.91        41.23 
TCGA-Z6-A8JD 
        3.42 

  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                         0.13                          1.55 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                        12.85                         13.38 
[1] "0.1 - 122.1 (12.8)" "1.6 - 83.2 (13.4)" 
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q23.3) MUTATED         6        2        3        0        23
  AMP PEAK  2(1Q23.3) WILD-TYPE       2        3        3        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q23.3) MUTATED          15        11          8          4
  AMP PEAK  2(1Q23.3) WILD-TYPE        16        14          6          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1Q23.3) MUTATED            3        3         4
  AMP PEAK  2(1Q23.3) WILD-TYPE          4        2         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             3
  STAGE IB                             3                             3
  STAGE II                             0                             1
  STAGE IIA                           23                            24
  STAGE IIB                           15                            16
  STAGE III                           11                            14
  STAGE IIIA                           8                             6
  STAGE IIIB                           4                             5
  STAGE IIIC                           3                             4
  STAGE IV                             3                             2
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  2(1Q23.3) MUTATED      21 22 41  1
  AMP PEAK  2(1Q23.3) WILD-TYPE    11 21 46  4
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  T0+T1                          21                            11
  T2                             22                            21
  T3                             41                            46
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q23.3) MUTATED   38 38  5  3
  AMP PEAK  2(1Q23.3) WILD-TYPE 39 30  7  5
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  N0                          38                            39
  N1                          38                            30
  N2                           5                             7
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED   67  7
  AMP PEAK  2(1Q23.3) WILD-TYPE 68  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED     67    7
  AMP PEAK  2(1Q23.3) WILD-TYPE   68    2
   clus
vv  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  0                          67                            68
  1                           7                             2
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED    8 85
  AMP PEAK  2(1Q23.3) WILD-TYPE 19 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED      8   85
  AMP PEAK  2(1Q23.3) WILD-TYPE   19   72
        clus
vv       AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  FEMALE                           8                            19
  MALE                            85                            72
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED   61 21
  AMP PEAK  2(1Q23.3) WILD-TYPE 62 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED     61   21
  AMP PEAK  2(1Q23.3) WILD-TYPE   62   22
     clus
vv    AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  NO                           61                            62
  YES                          21                            22
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED   44 49
  AMP PEAK  2(1Q23.3) WILD-TYPE 44 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED     44   49
  AMP PEAK  2(1Q23.3) WILD-TYPE   44   47
                                   clus
vv                                  AMP PEAK  2(1Q23.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          49
                                   clus
vv                                  AMP PEAK  2(1Q23.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            47
[1] 2 2
[1] FALSE
D2V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q23.3) MUTATED   76  3  1  2
  AMP PEAK  2(1Q23.3) WILD-TYPE 61  9  1  5
D2V12, multiclass
    clus
vv   AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  R0                          76                            61
  R1                           3                             9
  R2                           1                             1
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q23.3) MUTATED      28                         4    54
  AMP PEAK  2(1Q23.3) WILD-TYPE    18                         1    60
D2V14, multiclass
                           clus
vv                          AMP PEAK  2(1Q23.3) MUTATED
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              54
                           clus
vv                          AMP PEAK  2(1Q23.3) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED    3 51
  AMP PEAK  2(1Q23.3) WILD-TYPE  3 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED      3   51
  AMP PEAK  2(1Q23.3) WILD-TYPE    3   37
                        clus
vv                       AMP PEAK  2(1Q23.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       AMP PEAK  2(1Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            37
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q42.3) MUTATED   54 42
  AMP PEAK  3(1Q42.3) WILD-TYPE 54 34
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           96                            88 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           42                            34 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GN 
       60.39         0.36        25.78        31.27        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24         7.69        35.21         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D 
        4.67        14.50       122.10         3.68        47.38        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       25.22         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z 
        7.17         1.38         4.90         7.43         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.22         5.49        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        5.92        10.45        13.15        15.35        12.59        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.49        12.76        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        12.33        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.06        16.31        38.40         6.35        53.95        15.78 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EW 
       12.69        20.38         3.42        16.44         9.27         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       28.11        18.18        52.27        46.19        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        14.37         2.10         1.32         2.66        19.73 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GQ 
       20.02        14.30        58.55         7.63         5.92         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A6QS 
       32.45        33.27        20.78         3.88         9.30         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 
       14.86        12.16        44.75        68.02        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OJ 
       23.18        24.03         6.28         3.16        30.25        21.01 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.32         3.16        58.59        29.00         7.13        15.48 
TCGA-L5-A88W TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       25.12        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       13.41        83.24        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.38        12.62        12.46        12.59        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.85        25.25        10.52        12.03        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        8.02         7.59         7.04         9.30         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00         5.29        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G 
       22.82        12.43         1.55        18.31        33.70        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        41.23         3.42 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.13                          1.55 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       12.885                        13.395 
[1] "0.1 - 122.1 (12.9)" "1.6 - 83.2 (13.4)" 
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q42.3) MUTATED         4        2        4        0        23
  AMP PEAK  3(1Q42.3) WILD-TYPE       4        3        2        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          16        12          9          3
  AMP PEAK  3(1Q42.3) WILD-TYPE        15        13          5          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            4        3         4
  AMP PEAK  3(1Q42.3) WILD-TYPE          3        2         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             4                             2
  STAGE II                             0                             1
  STAGE IIA                           23                            24
  STAGE IIB                           16                            15
  STAGE III                           12                            13
  STAGE IIIA                           9                             5
  STAGE IIIB                           3                             6
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  3(1Q42.3) MUTATED      21 24 40  2
  AMP PEAK  3(1Q42.3) WILD-TYPE    11 19 47  3
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T0+T1                          21                            11
  T2                             24                            19
  T3                             40                            47
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  3(1Q42.3) MUTATED   36 42  4  4
  AMP PEAK  3(1Q42.3) WILD-TYPE 41 26  8  4
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          36                            41
  N1                          42                            26
  N2                           4                             8
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   69  7
  AMP PEAK  3(1Q42.3) WILD-TYPE 66  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     69    7
  AMP PEAK  3(1Q42.3) WILD-TYPE   66    2
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                          69                            66
  1                           7                             2
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED    7 89
  AMP PEAK  3(1Q42.3) WILD-TYPE 20 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      7   89
  AMP PEAK  3(1Q42.3) WILD-TYPE   20   68
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                           7                            20
  MALE                            89                            68
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   63 23
  AMP PEAK  3(1Q42.3) WILD-TYPE 60 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     63   23
  AMP PEAK  3(1Q42.3) WILD-TYPE   60   20
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  NO                           63                            60
  YES                          23                            20
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   43 53
  AMP PEAK  3(1Q42.3) WILD-TYPE 45 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     43   53
  AMP PEAK  3(1Q42.3) WILD-TYPE   45   43
                                   clus
vv                                  AMP PEAK  3(1Q42.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              43
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          53
                                   clus
vv                                  AMP PEAK  3(1Q42.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                45
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            43
[1] 2 2
[1] FALSE
D3V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(1Q42.3) MUTATED   72  4  2  2
  AMP PEAK  3(1Q42.3) WILD-TYPE 65  8  0  5
D3V12, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                          72                            65
  R1                           4                             8
  R2                           2                             0
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED      29                         4    57
  AMP PEAK  3(1Q42.3) WILD-TYPE    17                         1    57
D3V14, multiclass
                           clus
vv                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              57
                           clus
vv                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED    3 53
  AMP PEAK  3(1Q42.3) WILD-TYPE  3 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      3   53
  AMP PEAK  3(1Q42.3) WILD-TYPE    3   35
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            35
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2Q14.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(2Q14.2) MUTATED   40 20
  AMP PEAK  4(2Q14.2) WILD-TYPE 68 56
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           60                           124 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           20                            56 
$`AMP PEAK  4(2Q14.2) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-2H-A9GM TCGA-2H-A9GN 
       15.68         4.31         8.94         0.36        13.94         8.94 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93D 
       35.21         2.63        23.41        14.50        44.75        31.56 
TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX 
       25.22        32.61        47.93         3.32         1.38         7.43 
TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49P 
        2.60        55.50         8.71        52.57         5.92        12.33 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.38        13.25        12.62        12.49        12.85        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33        25.25        12.00        12.03        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        12.85        12.26         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       16.31         7.04         6.35        12.69        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY 
       16.44        15.35        25.81        27.09        28.11        33.70 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       46.19        18.21        25.08         3.42         1.32         2.66 

$`AMP PEAK  4(2Q14.2) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       60.39        34.85        18.28        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82        35.97        27.12         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        0.79        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       26.33        21.01        18.35         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       12.43        13.41        13.15        15.35        12.59        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       13.22         4.47        10.52        12.23        13.18        13.38 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       12.03        33.11         8.02        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW 
       15.78         2.89         2.30         7.00         5.29         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        8.98        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       41.23        14.37         2.10        19.73 

  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                         0.13                          0.30 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                         55.5                         122.1 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                       12.655                        13.220 
[1] "0.1 - 55.5 (12.7)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(2Q14.2) MUTATED         1        2        2        1        16
  AMP PEAK  4(2Q14.2) WILD-TYPE       7        3        4        0        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(2Q14.2) MUTATED          12         7          4          2
  AMP PEAK  4(2Q14.2) WILD-TYPE        19        18         10          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2Q14.2) MUTATED            2        0         1
  AMP PEAK  4(2Q14.2) WILD-TYPE          5        5         3
D4V3, multiclass
            clus
vv           AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                           16                            31
  STAGE IIB                           12                            19
  STAGE III                            7                            18
  STAGE IIIA                           4                            10
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             0                             5
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  4(2Q14.2) MUTATED       9 16 28  0
  AMP PEAK  4(2Q14.2) WILD-TYPE    23 27 59  5
D4V4, multiclass
       clus
vv      AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  T0+T1                           9                            23
  T2                             16                            27
  T3                             28                            59
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  4(2Q14.2) MUTATED   26 20  4  2
  AMP PEAK  4(2Q14.2) WILD-TYPE 51 48  8  6
D4V5, multiclass
    clus
vv   AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  N0                          26                            51
  N1                          20                            48
  N2                           4                             8
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED   43  1
  AMP PEAK  4(2Q14.2) WILD-TYPE 92  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED     43    1
  AMP PEAK  4(2Q14.2) WILD-TYPE   92    8
   clus
vv  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  0                          43                            92
  1                           1                             8
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q14.2) MUTATED     8  52
  AMP PEAK  4(2Q14.2) WILD-TYPE  19 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED      8   52
  AMP PEAK  4(2Q14.2) WILD-TYPE   19  105
        clus
vv       AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  FEMALE                           8                            19
  MALE                            52                           105
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED   39 16
  AMP PEAK  4(2Q14.2) WILD-TYPE 84 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED     39   16
  AMP PEAK  4(2Q14.2) WILD-TYPE   84   27
     clus
vv    AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  NO                           39                            84
  YES                          16                            27
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED   24 36
  AMP PEAK  4(2Q14.2) WILD-TYPE 64 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED     24   36
  AMP PEAK  4(2Q14.2) WILD-TYPE   64   60
                                   clus
vv                                  AMP PEAK  4(2Q14.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              24
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          36
                                   clus
vv                                  AMP PEAK  4(2Q14.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                64
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            60
[1] 2 2
[1] FALSE
D4V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(2Q14.2) MUTATED   46  0  0  3
  AMP PEAK  4(2Q14.2) WILD-TYPE 91 12  2  4
D4V12, multiclass
    clus
vv   AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  R0                          46                            91
  R1                           0                            12
  R2                           0                             2
  RX                           3                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2Q14.2) MUTATED      19                         3    33
  AMP PEAK  4(2Q14.2) WILD-TYPE    27                         2    81
D4V14, multiclass
                           clus
vv                          AMP PEAK  4(2Q14.2) MUTATED
  ASIAN                                              19
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              33
                           clus
vv                          AMP PEAK  4(2Q14.2) WILD-TYPE
  ASIAN                                                27
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED    2 35
  AMP PEAK  4(2Q14.2) WILD-TYPE  4 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED      2   35
  AMP PEAK  4(2Q14.2) WILD-TYPE    4   53
                        clus
vv                       AMP PEAK  4(2Q14.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          35
                        clus
vv                       AMP PEAK  4(2Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            53
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q31.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(2Q31.1) MUTATED   35 25
  AMP PEAK  5(2Q31.1) WILD-TYPE 73 51
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           60                           124 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           25                            51 
$`AMP PEAK  5(2Q31.1) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A88Y TCGA-2H-A9GJ TCGA-2H-A9GM 
       15.68        18.28         4.31         0.36        58.55        13.94 
TCGA-2H-A9GN TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        8.94         2.63         3.88        23.41         4.67        14.50 
TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88S 
       25.22        32.61        47.93         3.32         1.38        15.48 
TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49P 
        2.60        55.50        13.48        52.57         5.92        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A6 
       13.38        15.35        13.25        12.59        12.49        12.85 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.33        25.25        12.00        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.26         7.82         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        6.35        53.95        12.69        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A9VB 
       28.11        18.18        46.19        18.21        25.08         1.32 

$`AMP PEAK  5(2Q31.1) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       60.39        34.85         8.94        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82        35.97        27.12         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         7.63         5.92        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       26.33        21.01        18.35         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         7.43        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.75         3.02         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       12.43        13.41        13.15        12.59        12.62        12.46 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22         4.47        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6L6 
       12.33        13.38        12.03        33.11         8.02         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30         7.00         5.29 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8Q7 
        9.27         8.98        22.82         1.55        33.70        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05        11.24         9.17        15.91        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                         0.13                          0.30 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                        58.55                        122.10 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                       13.315                        12.790 
[1] "0.1 - 58.5 (13.3)"  "0.3 - 122.1 (12.8)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(2Q31.1) MUTATED         2        2        3        1        13
  AMP PEAK  5(2Q31.1) WILD-TYPE       6        3        3        0        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(2Q31.1) MUTATED           9         6          5          5
  AMP PEAK  5(2Q31.1) WILD-TYPE        22        19          9          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q31.1) MUTATED            2        1         1
  AMP PEAK  5(2Q31.1) WILD-TYPE          5        4         3
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             2                             3
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           13                            34
  STAGE IIB                            9                            22
  STAGE III                            6                            19
  STAGE IIIA                           5                             9
  STAGE IIIB                           5                             4
  STAGE IIIC                           2                             5
  STAGE IV                             1                             4
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  5(2Q31.1) MUTATED      11 11 29  1
  AMP PEAK  5(2Q31.1) WILD-TYPE    21 32 58  4
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  T0+T1                          11                            21
  T2                             11                            32
  T3                             29                            58
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  5(2Q31.1) MUTATED   24 19  6  2
  AMP PEAK  5(2Q31.1) WILD-TYPE 53 49  6  6
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  N0                          24                            53
  N1                          19                            49
  N2                           6                             6
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED   40  2
  AMP PEAK  5(2Q31.1) WILD-TYPE 95  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED     40    2
  AMP PEAK  5(2Q31.1) WILD-TYPE   95    7
   clus
vv  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  0                          40                            95
  1                           2                             7
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.1) MUTATED     5  55
  AMP PEAK  5(2Q31.1) WILD-TYPE  22 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED      5   55
  AMP PEAK  5(2Q31.1) WILD-TYPE   22  102
        clus
vv       AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  FEMALE                           5                            22
  MALE                            55                           102
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED   37 17
  AMP PEAK  5(2Q31.1) WILD-TYPE 86 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED     37   17
  AMP PEAK  5(2Q31.1) WILD-TYPE   86   26
     clus
vv    AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  NO                           37                            86
  YES                          17                            26
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED   25 35
  AMP PEAK  5(2Q31.1) WILD-TYPE 63 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED     25   35
  AMP PEAK  5(2Q31.1) WILD-TYPE   63   61
                                   clus
vv                                  AMP PEAK  5(2Q31.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              25
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          35
                                   clus
vv                                  AMP PEAK  5(2Q31.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                63
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            61
[1] 2 2
[1] FALSE
D5V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  5(2Q31.1) MUTATED   42  2  0  2
  AMP PEAK  5(2Q31.1) WILD-TYPE 95 10  2  5
D5V12, multiclass
    clus
vv   AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  R0                          42                            95
  R1                           2                            10
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q31.1) MUTATED      18                         3    34
  AMP PEAK  5(2Q31.1) WILD-TYPE    28                         2    80
D5V14, multiclass
                           clus
vv                          AMP PEAK  5(2Q31.1) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              34
                           clus
vv                          AMP PEAK  5(2Q31.1) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED    2 33
  AMP PEAK  5(2Q31.1) WILD-TYPE  4 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED      2   33
  AMP PEAK  5(2Q31.1) WILD-TYPE    4   55
                        clus
vv                       AMP PEAK  5(2Q31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       AMP PEAK  5(2Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            55
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(3Q26.2) MUTATED   77 51
  AMP PEAK  6(3Q26.2) WILD-TYPE 31 25
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          128                            56 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                           51                            25 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT 
       15.68        60.39         4.31        24.00        35.97        27.12 
TCGA-Q9-A6FU TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
        5.16        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FH 
        4.67        14.50        12.16        44.75         3.68        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON 
       23.18        25.22        30.25         0.30        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
       15.48         2.60         7.40        55.50         2.66        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G 
       13.22         5.49         8.71        13.41        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       12.33        13.38        13.15        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.26         8.02         7.59         5.06         6.35        53.95 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        2.89        12.69        20.38         3.42         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        1.32        19.73 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       34.85        18.28         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4QT 
        0.36        20.02        25.78        13.94         8.94         9.30 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       14.86       122.10        68.02        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         6.28         3.16        26.33        32.61        21.01 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
       58.59         4.90         7.43        25.12         3.75         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       12.92        13.48        13.55         7.76        21.37        83.24 
TCGA-L5-A8NW TCGA-LN-A49U TCGA-LN-A49X TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       46.09        15.35        12.62        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04        38.40         9.30        15.78         2.30         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29        16.44        15.35         1.55        46.19        18.21 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         0.13                          0.36 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       12.675                        15.350 
[1] "0.1 - 60.4 (12.7)"  "0.4 - 122.1 (15.3)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(3Q26.2) MUTATED         3        4        3        1        36
  AMP PEAK  6(3Q26.2) WILD-TYPE       5        1        3        0        11
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(3Q26.2) MUTATED          20        21         10          8
  AMP PEAK  6(3Q26.2) WILD-TYPE        11         4          4          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.2) MUTATED            5        3         3
  AMP PEAK  6(3Q26.2) WILD-TYPE          2        2         1
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             4                             1
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           36                            11
  STAGE IIB                           20                            11
  STAGE III                           21                             4
  STAGE IIIA                          10                             4
  STAGE IIIB                           8                             1
  STAGE IIIC                           5                             2
  STAGE IV                             3                             2
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  6(3Q26.2) MUTATED      16 33 64  4
  AMP PEAK  6(3Q26.2) WILD-TYPE    16 10 23  1
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  T0+T1                          16                            16
  T2                             33                            10
  T3                             64                            23
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  6(3Q26.2) MUTATED   54 46 10  6
  AMP PEAK  6(3Q26.2) WILD-TYPE 23 22  2  2
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  N0                          54                            23
  N1                          46                            22
  N2                          10                             2
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED   99  6
  AMP PEAK  6(3Q26.2) WILD-TYPE 36  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     99    6
  AMP PEAK  6(3Q26.2) WILD-TYPE   36    3
   clus
vv  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  0                          99                            36
  1                           6                             3
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED    16 112
  AMP PEAK  6(3Q26.2) WILD-TYPE  11  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     16  112
  AMP PEAK  6(3Q26.2) WILD-TYPE   11   45
        clus
vv       AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  FEMALE                          16                            11
  MALE                           112                            45
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED   83 33
  AMP PEAK  6(3Q26.2) WILD-TYPE 40 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     83   33
  AMP PEAK  6(3Q26.2) WILD-TYPE   40   10
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  NO                           83                            40
  YES                          33                            10
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED   46 82
  AMP PEAK  6(3Q26.2) WILD-TYPE 42 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     46   82
  AMP PEAK  6(3Q26.2) WILD-TYPE   42   14
                                   clus
vv                                  AMP PEAK  6(3Q26.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              46
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          82
                                   clus
vv                                  AMP PEAK  6(3Q26.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                42
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            14
[1] 2 2
[1] FALSE
D6V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(3Q26.2) MUTATED   100   7   2   4
  AMP PEAK  6(3Q26.2) WILD-TYPE  37   5   0   3
D6V12, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  R0                         100                            37
  R1                           7                             5
  R2                           2                             0
  RX                           4                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.2) MUTATED      43                         4    68
  AMP PEAK  6(3Q26.2) WILD-TYPE     3                         1    46
D6V14, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.2) MUTATED
  ASIAN                                              43
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              68
                           clus
vv                          AMP PEAK  6(3Q26.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED    4 70
  AMP PEAK  6(3Q26.2) WILD-TYPE  2 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      4   70
  AMP PEAK  6(3Q26.2) WILD-TYPE    2   18
                        clus
vv                       AMP PEAK  6(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       AMP PEAK  6(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            18
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4Q13.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(4Q13.3) MUTATED   25 11
  AMP PEAK  7(4Q13.3) WILD-TYPE 83 65
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           36                           148 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           11                            65 
$`AMP PEAK  7(4Q13.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-S8-A6BV TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A50L 
       18.28         4.31        20.02        20.78         2.63         0.53 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-L5-A4ON TCGA-L5-A4OO 
       23.41        12.82       122.10        44.75        18.35         3.32 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49O 
       55.50         5.49         8.71        83.24        10.85        13.41 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HX 
       13.38        13.25        12.62        15.52        11.54        12.23 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-V5-A7RC 
       12.03        13.18        12.85         7.82         9.30         3.42 
TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE 
       25.81         8.12        18.05        11.24        18.21         2.10 

$`AMP PEAK  7(4Q13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        35.21         0.85        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30        17.03         0.79         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.50        12.16        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76        21.37        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       12.43        12.33        13.15        15.35        12.59        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       46.19         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         1.32         2.66        19.73 

  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                         0.53                          0.13 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                       122.10                         68.02 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                       12.835                        13.165 
[1] "0.5 - 122.1 (12.8)" "0.1 - 68.0 (13.2)" 
[1] "hr=" "1.5"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(4Q13.3) MUTATED         1        0        0        0         9
  AMP PEAK  7(4Q13.3) WILD-TYPE       7        5        6        1        38
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(4Q13.3) MUTATED           5         5          7          3
  AMP PEAK  7(4Q13.3) WILD-TYPE        26        20          7          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(4Q13.3) MUTATED            1        1         0
  AMP PEAK  7(4Q13.3) WILD-TYPE          6        4         4
D7V3, multiclass
            clus
vv           AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             5
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                            9                            38
  STAGE IIB                            5                            26
  STAGE III                            5                            20
  STAGE IIIA                           7                             7
  STAGE IIIB                           3                             6
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(4Q13.3) MUTATED       3  8 21  1
  AMP PEAK  7(4Q13.3) WILD-TYPE    29 35 66  4
D7V4, multiclass
       clus
vv      AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  T0+T1                           3                            29
  T2                              8                            35
  T3                             21                            66
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  7(4Q13.3) MUTATED   13 14  4  2
  AMP PEAK  7(4Q13.3) WILD-TYPE 64 54  8  6
D7V5, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  N0                          13                            64
  N1                          14                            54
  N2                           4                             8
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q13.3) MUTATED    27   1
  AMP PEAK  7(4Q13.3) WILD-TYPE 108   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED     27    1
  AMP PEAK  7(4Q13.3) WILD-TYPE  108    8
   clus
vv  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  0                          27                           108
  1                           1                             8
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q13.3) MUTATED     5  31
  AMP PEAK  7(4Q13.3) WILD-TYPE  22 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED      5   31
  AMP PEAK  7(4Q13.3) WILD-TYPE   22  126
        clus
vv       AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  FEMALE                           5                            22
  MALE                            31                           126
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q13.3) MUTATED    19  11
  AMP PEAK  7(4Q13.3) WILD-TYPE 104  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED     19   11
  AMP PEAK  7(4Q13.3) WILD-TYPE  104   32
     clus
vv    AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  NO                           19                           104
  YES                          11                            32
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, binary
                               cls
clus                             0  1
  AMP PEAK  7(4Q13.3) MUTATED   12 24
  AMP PEAK  7(4Q13.3) WILD-TYPE 76 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED     12   24
  AMP PEAK  7(4Q13.3) WILD-TYPE   76   72
                                   clus
vv                                  AMP PEAK  7(4Q13.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              12
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          24
                                   clus
vv                                  AMP PEAK  7(4Q13.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            72
[1] 2 2
[1] FALSE
D7V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(4Q13.3) MUTATED    26   1   0   3
  AMP PEAK  7(4Q13.3) WILD-TYPE 111  11   2   4
D7V12, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  R0                          26                           111
  R1                           1                            11
  R2                           0                             2
  RX                           3                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q13.3) MUTATED      14                         2    19
  AMP PEAK  7(4Q13.3) WILD-TYPE    32                         3    95
D7V14, multiclass
                           clus
vv                          AMP PEAK  7(4Q13.3) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              19
                           clus
vv                          AMP PEAK  7(4Q13.3) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                               cls
clus                             0  1
  AMP PEAK  7(4Q13.3) MUTATED    1 20
  AMP PEAK  7(4Q13.3) WILD-TYPE  5 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED      1   20
  AMP PEAK  7(4Q13.3) WILD-TYPE    5   68
                        clus
vv                       AMP PEAK  7(4Q13.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       AMP PEAK  7(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            68
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(5P15.33) MUTATED   65 33
  AMP PEAK  8(5P15.33) WILD-TYPE 43 43
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            98                             86 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            33                             43 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG 
       18.28         4.31         8.94        19.99         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 
       27.12         5.16        14.30         5.92        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12        18.64         0.53         0.79        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        4.67        14.50        44.75        68.02         3.68        47.38 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM 
       31.56        25.22         3.16         0.30        32.61        47.93 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        7.17         3.16         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60         3.75        55.50        12.92        16.47        13.55 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O 
       13.41        52.57        10.85        10.36         5.92        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.59        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       12.85        12.26         5.06        16.31        38.40        53.95 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO 
       15.78         7.00        20.38         3.42        16.44        25.81 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       27.09        18.31        33.70        18.18        52.27        18.05 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        25.08        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        60.39        34.85        24.00         4.70        22.82 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.02        25.78        31.27        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24         4.21         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       14.86        12.16       122.10        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
       24.03         6.28        30.25        26.33        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        3.32         1.38        58.59         7.43        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02         2.66        13.48        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M 
       21.37         8.71        83.24        46.09        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 
       12.43        12.33        12.59        12.49        12.76        11.54 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.03        33.11         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04         6.35         9.30         2.89         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER 
        5.29        15.35         9.27         8.98        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55         8.12        28.11        46.19        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T7 
       18.21        41.23 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.30                           0.13 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         68.02                         122.10 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                        13.315                         12.540 
[1] "0.3 - 68.0 (13.3)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.4"
D8V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(5P15.33) MUTATED         1        3        4        1        29
  AMP PEAK  8(5P15.33) WILD-TYPE       7        2        2        0        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(5P15.33) MUTATED          15        13          9          3
  AMP PEAK  8(5P15.33) WILD-TYPE        16        12          5          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            5        4         1
  AMP PEAK  8(5P15.33) WILD-TYPE          2        1         3
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              3                              2
  STAGE IB                              4                              2
  STAGE II                              1                              0
  STAGE IIA                            29                             18
  STAGE IIB                            15                             16
  STAGE III                            13                             12
  STAGE IIIA                            9                              5
  STAGE IIIB                            3                              6
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  8(5P15.33) MUTATED      10 23 57  1
  AMP PEAK  8(5P15.33) WILD-TYPE    22 20 30  4
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                           10                             22
  T2                              23                             20
  T3                              57                             30
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK  8(5P15.33) MUTATED   45 35  5  5
  AMP PEAK  8(5P15.33) WILD-TYPE 32 33  7  3
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  N0                           45                             32
  N1                           35                             33
  N2                            5                              7
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   73  5
  AMP PEAK  8(5P15.33) WILD-TYPE 62  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     73    5
  AMP PEAK  8(5P15.33) WILD-TYPE   62    4
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                           73                             62
  1                            5                              4
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   13 85
  AMP PEAK  8(5P15.33) WILD-TYPE 14 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     13   85
  AMP PEAK  8(5P15.33) WILD-TYPE   14   72
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           13                             14
  MALE                             85                             72
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   63 26
  AMP PEAK  8(5P15.33) WILD-TYPE 60 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     63   26
  AMP PEAK  8(5P15.33) WILD-TYPE   60   17
     clus
vv    AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  NO                            63                             60
  YES                           26                             17
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   35 63
  AMP PEAK  8(5P15.33) WILD-TYPE 53 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     35   63
  AMP PEAK  8(5P15.33) WILD-TYPE   53   33
                                   clus
vv                                  AMP PEAK  8(5P15.33) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               35
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           63
                                   clus
vv                                  AMP PEAK  8(5P15.33) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 53
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             33
[1] 2 2
[1] FALSE
D8V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  8(5P15.33) MUTATED   73  8  2  4
  AMP PEAK  8(5P15.33) WILD-TYPE 64  4  0  3
D8V12, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  R0                           73                             64
  R1                            8                              4
  R2                            2                              0
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED      33                         4    56
  AMP PEAK  8(5P15.33) WILD-TYPE    13                         1    58
D8V14, multiclass
                           clus
vv                          AMP PEAK  8(5P15.33) MUTATED
  ASIAN                                               33
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               56
                           clus
vv                          AMP PEAK  8(5P15.33) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED    2 53
  AMP PEAK  8(5P15.33) WILD-TYPE  4 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      2   53
  AMP PEAK  8(5P15.33) WILD-TYPE    4   35
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(6P21.1) MUTATED   35 34
  AMP PEAK  9(6P21.1) WILD-TYPE 73 42
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           69                           115 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           34                            42 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF 
       60.39         0.36        35.97        27.12        20.02        25.78 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        4.21         3.88         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       68.02        21.70        30.25        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        1.38        58.59         7.13        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN 
        3.02        55.50         2.66        12.92        13.48         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       21.37        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 
       13.41        13.15        12.59        12.62        12.49        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FR 
       12.33        12.33        12.00        12.23        13.18        12.26 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        8.02         7.59        16.31         7.04        38.40        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA7I 
       15.78         2.89         3.42         8.98        22.82        15.91 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08         2.10         1.32 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU TCGA-2H-A9GH TCGA-2H-A9GL 
        4.70        19.99        22.82         5.16        31.27         5.92 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        47.38        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
       21.01         3.32         3.16         4.90        29.00         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       25.12         7.40        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N 
        8.71        13.41        83.24        46.09        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.33        13.38        15.35        13.25        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
       12.76        12.59        22.39        12.85        15.52        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        25.25        10.52        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.38         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        5.06         6.35         9.30         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         5.29        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
        9.17        18.21        41.23        14.37         3.42         2.66 
TCGA-ZR-A9CJ 
       19.73 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         0.36                          0.13 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                        12.59                         13.22 
[1] "0.4 - 122.1 (12.6)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.2"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6P21.1) MUTATED         5        2        1        0        15
  AMP PEAK  9(6P21.1) WILD-TYPE       3        3        5        1        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6P21.1) MUTATED          11        12          4          2
  AMP PEAK  9(6P21.1) WILD-TYPE        20        13         10          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P21.1) MUTATED            1        1         3
  AMP PEAK  9(6P21.1) WILD-TYPE          6        4         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           15                            32
  STAGE IIB                           11                            20
  STAGE III                           12                            13
  STAGE IIIA                           4                            10
  STAGE IIIB                           2                             7
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  9(6P21.1) MUTATED      13 15 30  1
  AMP PEAK  9(6P21.1) WILD-TYPE    19 28 57  4
D9V4, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T0+T1                          13                            19
  T2                             15                            28
  T3                             30                            57
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  9(6P21.1) MUTATED   28 27  3  1
  AMP PEAK  9(6P21.1) WILD-TYPE 49 41  9  7
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                          28                            49
  N1                          27                            41
  N2                           3                             9
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED   46  4
  AMP PEAK  9(6P21.1) WILD-TYPE 89  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     46    4
  AMP PEAK  9(6P21.1) WILD-TYPE   89    5
   clus
vv  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  0                          46                            89
  1                           4                             5
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED    8 61
  AMP PEAK  9(6P21.1) WILD-TYPE 19 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      8   61
  AMP PEAK  9(6P21.1) WILD-TYPE   19   96
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                           8                            19
  MALE                            61                            96
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED   44 16
  AMP PEAK  9(6P21.1) WILD-TYPE 79 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     44   16
  AMP PEAK  9(6P21.1) WILD-TYPE   79   27
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  NO                           44                            79
  YES                          16                            27
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED   42 27
  AMP PEAK  9(6P21.1) WILD-TYPE 46 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     42   27
  AMP PEAK  9(6P21.1) WILD-TYPE   46   69
                                   clus
vv                                  AMP PEAK  9(6P21.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              42
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          27
                                   clus
vv                                  AMP PEAK  9(6P21.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                46
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            69
[1] 2 2
[1] FALSE
D9V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  9(6P21.1) MUTATED   53  3  1  1
  AMP PEAK  9(6P21.1) WILD-TYPE 84  9  1  6
D9V12, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  R0                          53                            84
  R1                           3                             9
  R2                           1                             1
  RX                           1                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6P21.1) MUTATED      17                         3    40
  AMP PEAK  9(6P21.1) WILD-TYPE    29                         2    74
D9V14, multiclass
                           clus
vv                          AMP PEAK  9(6P21.1) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              40
                           clus
vv                          AMP PEAK  9(6P21.1) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED    1 32
  AMP PEAK  9(6P21.1) WILD-TYPE  5 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      1   32
  AMP PEAK  9(6P21.1) WILD-TYPE    5   56
                        clus
vv                       AMP PEAK  9(6P21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       AMP PEAK  9(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            56
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6Q23.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(6Q23.3) MUTATED   20 22
  AMP PEAK 10(6Q23.3) WILD-TYPE 88 54
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           42                           142 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           22                            54 
$`AMP PEAK 10(6Q23.3) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OG TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GI 
       60.39        34.85         4.70        27.12        31.27        14.30 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E 
       13.94        16.24         3.88       122.10        68.02        30.25 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.13         7.43        15.48         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ 
        2.66        12.92        13.48        21.37        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY 
       10.45        13.15        12.59         4.47        10.52        12.03 
TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
       13.18        33.11         8.02        16.31         7.04        15.78 
TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.31        18.18        11.24        15.91         2.10        19.73 

$`AMP PEAK 10(6Q23.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI 
       15.68        18.28         4.31         8.94        24.00        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55         7.63         5.92         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NK 
       29.00         2.60        25.12         7.40        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.38        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.00        12.23        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        12.85        12.26         7.82         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       12.43         1.55         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       46.19        18.05         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         3.42         1.32         2.66 

  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                         2.10                          0.13 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                       13.330                        12.835 
[1] "2.1 - 122.1 (13.3)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(6Q23.3) MUTATED         5        0        1        0         8
  AMP PEAK 10(6Q23.3) WILD-TYPE       3        5        5        1        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(6Q23.3) MUTATED           7         4          1          1
  AMP PEAK 10(6Q23.3) WILD-TYPE        24        21         13          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6Q23.3) MUTATED            3        4         3
  AMP PEAK 10(6Q23.3) WILD-TYPE          4        1         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             0                             5
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                            8                            39
  STAGE IIB                            7                            24
  STAGE III                            4                            21
  STAGE IIIA                           1                            13
  STAGE IIIB                           1                             8
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 10(6Q23.3) MUTATED      10  7 20  1
  AMP PEAK 10(6Q23.3) WILD-TYPE    22 36 67  4
D10V4, multiclass
       clus
vv      AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  T0+T1                          10                            22
  T2                              7                            36
  T3                             20                            67
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 10(6Q23.3) MUTATED   19 14  1  4
  AMP PEAK 10(6Q23.3) WILD-TYPE 58 54 11  4
D10V5, multiclass
    clus
vv   AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  N0                          19                            58
  N1                          14                            54
  N2                           1                            11
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6Q23.3) MUTATED    28   7
  AMP PEAK 10(6Q23.3) WILD-TYPE 107   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED     28    7
  AMP PEAK 10(6Q23.3) WILD-TYPE  107    2
   clus
vv  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  0                          28                           107
  1                           7                             2
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6Q23.3) MUTATED     6  36
  AMP PEAK 10(6Q23.3) WILD-TYPE  21 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED      6   36
  AMP PEAK 10(6Q23.3) WILD-TYPE   21  121
        clus
vv       AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  FEMALE                           6                            21
  MALE                            36                           121
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED   30  9
  AMP PEAK 10(6Q23.3) WILD-TYPE 93 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED     30    9
  AMP PEAK 10(6Q23.3) WILD-TYPE   93   34
     clus
vv    AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  NO                           30                            93
  YES                           9                            34
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED   26 16
  AMP PEAK 10(6Q23.3) WILD-TYPE 62 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED     26   16
  AMP PEAK 10(6Q23.3) WILD-TYPE   62   80
                                   clus
vv                                  AMP PEAK 10(6Q23.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              26
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          16
                                   clus
vv                                  AMP PEAK 10(6Q23.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            80
[1] 2 2
[1] FALSE
D10V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(6Q23.3) MUTATED    31   2   2   1
  AMP PEAK 10(6Q23.3) WILD-TYPE 106  10   0   6
D10V12, multiclass
    clus
vv   AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  R0                          31                           106
  R1                           2                            10
  R2                           2                             0
  RX                           1                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6Q23.3) MUTATED       8                         1    27
  AMP PEAK 10(6Q23.3) WILD-TYPE    38                         4    87
D10V14, multiclass
                           clus
vv                          AMP PEAK 10(6Q23.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              27
                           clus
vv                          AMP PEAK 10(6Q23.3) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED    0 16
  AMP PEAK 10(6Q23.3) WILD-TYPE  6 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED      0   16
  AMP PEAK 10(6Q23.3) WILD-TYPE    6   72
                        clus
vv                       AMP PEAK 10(6Q23.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK 10(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            72
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 11(7P11.2) MUTATED   77 48
  AMP PEAK 11(7P11.2) WILD-TYPE 31 28
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          125                            59 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           48                            28 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       60.39        18.28         4.31        24.00         4.70        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
        0.36        35.97        27.12         5.16        20.02        25.78 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
        7.63         5.92        13.94         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
        7.69        35.21         0.85        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       17.03         0.79        23.41        14.50        44.75        68.02 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       21.70        23.18        25.22         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       15.52        12.33        13.22        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.03        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04        53.95         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        8.98        25.81        27.09         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        18.18        52.27        46.19        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        14.37         1.32         2.66        19.73 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OI TCGA-2H-A9GH TCGA-2H-A9GI 
       15.68        34.85         8.94        19.99        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
       58.55         4.21        33.27        20.78         2.63         3.88 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        9.30        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93F 
      122.10         3.68        41.52        47.38        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI 
        6.28         7.17         7.43        25.12         7.40        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.76        21.37        83.24        10.45        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.33        13.15        22.39        11.54         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A6XQ 
       12.23        13.18        13.38        33.11        38.40         6.35 
TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-AA4G 
       15.78        16.44        22.82        12.43        18.31        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        41.23         3.42         2.10 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         0.13                          2.10 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        12.92                         13.15 
[1] "0.1 - 68.0 (12.9)"  "2.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         6        2        4        1        28
  AMP PEAK 11(7P11.2) WILD-TYPE       2        3        2        0        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          23        18          9          6
  AMP PEAK 11(7P11.2) WILD-TYPE         8         7          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(7P11.2) MUTATED            4        2         3
  AMP PEAK 11(7P11.2) WILD-TYPE          3        3         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             3
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           28                            19
  STAGE IIB                           23                             8
  STAGE III                           18                             7
  STAGE IIIA                           9                             5
  STAGE IIIB                           6                             3
  STAGE IIIC                           4                             3
  STAGE IV                             2                             3
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 11(7P11.2) MUTATED      23 23 62  2
  AMP PEAK 11(7P11.2) WILD-TYPE     9 20 25  3
D11V4, multiclass
       clus
vv      AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T0+T1                          23                             9
  T2                             23                            20
  T3                             62                            25
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   49 49  7  4
  AMP PEAK 11(7P11.2) WILD-TYPE 28 19  5  4
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          49                            28
  N1                          49                            19
  N2                           7                             5
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   87  5
  AMP PEAK 11(7P11.2) WILD-TYPE 48  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     87    5
  AMP PEAK 11(7P11.2) WILD-TYPE   48    4
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                          87                            48
  1                           5                             4
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    16 109
  AMP PEAK 11(7P11.2) WILD-TYPE  11  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     16  109
  AMP PEAK 11(7P11.2) WILD-TYPE   11   48
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          16                            11
  MALE                           109                            48
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   85 26
  AMP PEAK 11(7P11.2) WILD-TYPE 38 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     85   26
  AMP PEAK 11(7P11.2) WILD-TYPE   38   17
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  NO                           85                            38
  YES                          26                            17
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   65 60
  AMP PEAK 11(7P11.2) WILD-TYPE 23 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     65   60
  AMP PEAK 11(7P11.2) WILD-TYPE   23   36
                                   clus
vv                                  AMP PEAK 11(7P11.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          60
                                   clus
vv                                  AMP PEAK 11(7P11.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            36
[1] 2 2
[1] FALSE
D11V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 11(7P11.2) MUTATED   89  9  1  5
  AMP PEAK 11(7P11.2) WILD-TYPE 48  3  1  2
D11V12, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  R0                          89                            48
  R1                           9                             3
  R2                           1                             1
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7P11.2) MUTATED      32                         5    77
  AMP PEAK 11(7P11.2) WILD-TYPE    14                         0    37
D11V14, multiclass
                           clus
vv                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                              32
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              77
                           clus
vv                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED    5 58
  AMP PEAK 11(7P11.2) WILD-TYPE  1 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      5   58
  AMP PEAK 11(7P11.2) WILD-TYPE    1   30
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            30
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(7Q21.2) MUTATED   69 45
  AMP PEAK 12(7Q21.2) WILD-TYPE 39 31
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          114                            70 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           45                            31 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39        18.28        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       27.12        31.27         8.94        16.24        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       35.21         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       23.41         9.96        14.50        44.75        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       47.38        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       30.25         0.30        32.61        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
       16.47        13.55        13.22        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P 
       10.85        10.36         5.92        10.45        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       11.54        12.33        12.33        25.25        12.00        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.33        13.18         0.13        12.85         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59         7.04        38.40         6.35         9.30         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        27.09         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        9.17        18.21        25.08         2.10         1.32        19.73 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85         4.31         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        5.16        20.02        25.78        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        5.92        13.94         4.21        33.27         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OF 
       12.16       122.10        41.52        24.03         6.28        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
       21.01         7.17         7.43        25.12         7.40        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.48         7.76         5.49        21.37         8.71        83.24 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.66        12.43        13.25        22.39        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR 
       10.52        12.23        13.18        13.38        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC 
       33.11         5.06        16.31        53.95        15.78         2.30 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I 
       16.44         8.98        22.82        12.43        52.27        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.66 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         0.13                          0.79 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                       12.805                        13.315 
[1] "0.1 - 68.0 (12.8)"  "0.8 - 122.1 (13.3)"
[1] "hr=" "1"  
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         5        2        3        1        29
  AMP PEAK 12(7Q21.2) WILD-TYPE       3        3        3        0        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          18        12          9          6
  AMP PEAK 12(7Q21.2) WILD-TYPE        13        13          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(7Q21.2) MUTATED            6        4         3
  AMP PEAK 12(7Q21.2) WILD-TYPE          1        1         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           29                            18
  STAGE IIB                           18                            13
  STAGE III                           12                            13
  STAGE IIIA                           9                             5
  STAGE IIIB                           6                             3
  STAGE IIIC                           6                             1
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 12(7Q21.2) MUTATED      21 23 58  0
  AMP PEAK 12(7Q21.2) WILD-TYPE    11 20 29  5
D12V4, multiclass
       clus
vv      AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T0+T1                          21                            11
  T2                             23                            20
  T3                             58                            29
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 12(7Q21.2) MUTATED   45 41  8  7
  AMP PEAK 12(7Q21.2) WILD-TYPE 32 27  4  1
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          45                            32
  N1                          41                            27
  N2                           8                             4
  N3                           7                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   80  7
  AMP PEAK 12(7Q21.2) WILD-TYPE 55  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     80    7
  AMP PEAK 12(7Q21.2) WILD-TYPE   55    2
   clus
vv  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  0                          80                            55
  1                           7                             2
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7Q21.2) MUTATED    14 100
  AMP PEAK 12(7Q21.2) WILD-TYPE  13  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     14  100
  AMP PEAK 12(7Q21.2) WILD-TYPE   13   57
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          14                            13
  MALE                           100                            57
[1] 2 2
[1] FALSE
D12V8, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   75 28
  AMP PEAK 12(7Q21.2) WILD-TYPE 48 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     75   28
  AMP PEAK 12(7Q21.2) WILD-TYPE   48   15
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  NO                           75                            48
  YES                          28                            15
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   55 59
  AMP PEAK 12(7Q21.2) WILD-TYPE 33 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     55   59
  AMP PEAK 12(7Q21.2) WILD-TYPE   33   37
                                   clus
vv                                  AMP PEAK 12(7Q21.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              55
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          59
                                   clus
vv                                  AMP PEAK 12(7Q21.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                33
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            37
[1] 2 2
[1] FALSE
D12V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 12(7Q21.2) MUTATED   87  7  0  4
  AMP PEAK 12(7Q21.2) WILD-TYPE 50  5  2  3
D12V12, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  R0                          87                            50
  R1                           7                             5
  R2                           0                             2
  RX                           4                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(7Q21.2) MUTATED      32                         4    70
  AMP PEAK 12(7Q21.2) WILD-TYPE    14                         1    44
D12V14, multiclass
                           clus
vv                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                              32
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              70
                           clus
vv                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED    4 54
  AMP PEAK 12(7Q21.2) WILD-TYPE  2 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      4   54
  AMP PEAK 12(7Q21.2) WILD-TYPE    2   34
                        clus
vv                       AMP PEAK 12(7Q21.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       AMP PEAK 12(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            34
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8P23.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 13(8P23.1) MUTATED   26 26
  AMP PEAK 13(8P23.1) WILD-TYPE 82 50
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           52                           132 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           26                            50 
$`AMP PEAK 13(8P23.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88Y TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN 
       18.28        19.99         0.36        25.78        14.30         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A8O2 
       16.24        32.45        33.27        35.21        20.78         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
      122.10        68.02        21.70        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25         0.30        21.01        47.93        18.35 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK 
        3.16         4.90         7.13        55.50        12.92        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49K 
        7.76         5.49        21.37         8.71        10.36         5.92 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A7HZ TCGA-R6-A6DQ TCGA-R6-A6KZ 
       15.35        12.59        12.62        13.18         7.59         5.06 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP 
       15.78        12.69         7.00        16.44        15.35        27.09 
TCGA-VR-A8EQ TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-ZR-A9CJ 
       22.82        18.21        25.08        19.73 

$`AMP PEAK 13(8P23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82        35.97        27.12         5.16        20.02 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       31.27        58.55         7.63         5.92        13.94         4.21 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        7.69         0.85         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
        9.96        14.86        14.50        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH 
       41.52        47.38        23.18         6.28        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         7.17         1.38        58.59        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU 
        2.66        13.48        16.47        13.22        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.85        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
       13.41        12.33        13.38        13.15        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        12.03        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         8.02        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW 
        6.35        53.95         9.30         2.89         2.30        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        5.29         3.42         9.27         8.98        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 

  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                         0.30                          0.13 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                        16.01                         12.59 
[1] "0.3 - 122.1 (16.0)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8P23.1) MUTATED         3        2        2        0        11
  AMP PEAK 13(8P23.1) WILD-TYPE       5        3        4        1        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8P23.1) MUTATED           8         7          3          2
  AMP PEAK 13(8P23.1) WILD-TYPE        23        18         11          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(8P23.1) MUTATED            4        2         2
  AMP PEAK 13(8P23.1) WILD-TYPE          3        3         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           11                            36
  STAGE IIB                            8                            23
  STAGE III                            7                            18
  STAGE IIIA                           3                            11
  STAGE IIIB                           2                             7
  STAGE IIIC                           4                             3
  STAGE IV                             2                             3
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 13(8P23.1) MUTATED      12  9 26  1
  AMP PEAK 13(8P23.1) WILD-TYPE    20 34 61  4
D13V4, multiclass
       clus
vv      AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  T0+T1                          12                            20
  T2                              9                            34
  T3                             26                            61
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 13(8P23.1) MUTATED   22 20  2  4
  AMP PEAK 13(8P23.1) WILD-TYPE 55 48 10  4
D13V5, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  N0                          22                            55
  N1                          20                            48
  N2                           2                            10
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(8P23.1) MUTATED    34   4
  AMP PEAK 13(8P23.1) WILD-TYPE 101   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     34    4
  AMP PEAK 13(8P23.1) WILD-TYPE  101    5
   clus
vv  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  0                          34                           101
  1                           4                             5
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(8P23.1) MUTATED    11  41
  AMP PEAK 13(8P23.1) WILD-TYPE  16 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     11   41
  AMP PEAK 13(8P23.1) WILD-TYPE   16  116
        clus
vv       AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  FEMALE                          11                            16
  MALE                            41                           116
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                             0  1
  AMP PEAK 13(8P23.1) MUTATED   37  9
  AMP PEAK 13(8P23.1) WILD-TYPE 86 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     37    9
  AMP PEAK 13(8P23.1) WILD-TYPE   86   34
     clus
vv    AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  NO                           37                            86
  YES                           9                            34
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, binary
                               cls
clus                             0  1
  AMP PEAK 13(8P23.1) MUTATED   34 18
  AMP PEAK 13(8P23.1) WILD-TYPE 54 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     34   18
  AMP PEAK 13(8P23.1) WILD-TYPE   54   78
                                   clus
vv                                  AMP PEAK 13(8P23.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              34
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          18
                                   clus
vv                                  AMP PEAK 13(8P23.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            78
[1] 2 2
[1] FALSE
D13V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 13(8P23.1) MUTATED   39  8  0  0
  AMP PEAK 13(8P23.1) WILD-TYPE 98  4  2  7
D13V12, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  R0                          39                            98
  R1                           8                             4
  R2                           0                             2
  RX                           0                             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"
D13V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8P23.1) MUTATED       7                         2    36
  AMP PEAK 13(8P23.1) WILD-TYPE    39                         3    78
D13V14, multiclass
                           clus
vv                          AMP PEAK 13(8P23.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              36
                           clus
vv                          AMP PEAK 13(8P23.1) WILD-TYPE
  ASIAN                                                39
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                               cls
clus                             0  1
  AMP PEAK 13(8P23.1) MUTATED    2 18
  AMP PEAK 13(8P23.1) WILD-TYPE  4 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED      2   18
  AMP PEAK 13(8P23.1) WILD-TYPE    4   70
                        clus
vv                       AMP PEAK 13(8P23.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK 13(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            70
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8P11.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(8P11.21) MUTATED   48 38
  AMP PEAK 14(8P11.21) WILD-TYPE 60 38
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            86                             98 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            38                             38 
$`AMP PEAK 14(8P11.21) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        18.28        19.99         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       20.02        14.30        58.55        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS 
        4.21        33.27        35.21        20.78        18.64         3.88 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       17.03        12.82         4.67       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
        3.68        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.30        26.33        47.93        18.35         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NK TCGA-L5-A8NL 
        4.90         7.13         7.43         3.75        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L7-A6VZ 
        7.76         5.49        21.37         8.71        13.41        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        5.92        10.45        12.33        13.15        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.62        12.46        12.76        12.59        12.85        11.54 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33        10.52        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 
        0.13        12.85        12.26         7.59         5.06        53.95 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX 
       15.78        12.69         7.00        20.38        15.35         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D 
       27.09        22.82         8.12        28.11        18.18        46.19 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`AMP PEAK 14(8P11.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL 
       22.82         5.16        25.78        31.27         7.63         5.92 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT 
       32.45         7.69         0.85         2.63        20.12         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.53         0.79        23.41         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       12.16        41.52        47.38        21.70        25.22         6.28 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       32.61        21.01         7.17         1.38        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV 
        2.66        12.92        13.48        16.47        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.85        12.66        12.43        13.41        13.38 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR 
       13.25        12.59        12.49        22.39        15.52        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 
        4.47        12.33        25.25        12.00        12.23        13.38 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.03        33.11         7.82         8.02        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB 
       38.40         6.35         9.30         2.89         2.30         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        16.44         9.27        25.81        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.31        33.70        52.27        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                          0.13                           0.53 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                         13.00                          13.07 
[1] "0.1 - 122.1 (13.0)" "0.5 - 83.2 (13.1)" 
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P11.21) MUTATED         4        2        2        1        20
  AMP PEAK 14(8P11.21) WILD-TYPE       4        3        4        0        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P11.21) MUTATED          15        15          4          6
  AMP PEAK 14(8P11.21) WILD-TYPE        16        10         10          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(8P11.21) MUTATED            5        1         3
  AMP PEAK 14(8P11.21) WILD-TYPE          2        4         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            20                             27
  STAGE IIB                            15                             16
  STAGE III                            15                             10
  STAGE IIIA                            4                             10
  STAGE IIIB                            6                              3
  STAGE IIIC                            5                              2
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 14(8P11.21) MUTATED      14 19 45  2
  AMP PEAK 14(8P11.21) WILD-TYPE    18 24 42  3
D14V4, multiclass
       clus
vv      AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  T0+T1                           14                             18
  T2                              19                             24
  T3                              45                             42
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 14(8P11.21) MUTATED   35 34  6  5
  AMP PEAK 14(8P11.21) WILD-TYPE 42 34  6  3
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  N0                           35                             42
  N1                           34                             34
  N2                            6                              6
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   65  4
  AMP PEAK 14(8P11.21) WILD-TYPE 70  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     65    4
  AMP PEAK 14(8P11.21) WILD-TYPE   70    5
   clus
vv  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  0                           65                             70
  1                            4                              5
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   11 75
  AMP PEAK 14(8P11.21) WILD-TYPE 16 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     11   75
  AMP PEAK 14(8P11.21) WILD-TYPE   16   82
        clus
vv       AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  FEMALE                           11                             16
  MALE                             75                             82
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   55 21
  AMP PEAK 14(8P11.21) WILD-TYPE 68 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     55   21
  AMP PEAK 14(8P11.21) WILD-TYPE   68   22
     clus
vv    AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  NO                            55                             68
  YES                           21                             22
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   42 44
  AMP PEAK 14(8P11.21) WILD-TYPE 46 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     42   44
  AMP PEAK 14(8P11.21) WILD-TYPE   46   52
                                   clus
vv                                  AMP PEAK 14(8P11.21) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               42
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           44
                                   clus
vv                                  AMP PEAK 14(8P11.21) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 46
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             52
[1] 2 2
[1] FALSE
D14V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(8P11.21) MUTATED   67  7  1  2
  AMP PEAK 14(8P11.21) WILD-TYPE 70  5  1  5
D14V12, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  R0                           67                             70
  R1                            7                              5
  R2                            1                              1
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8P11.21) MUTATED      27                         1    49
  AMP PEAK 14(8P11.21) WILD-TYPE    19                         4    65
D14V14, multiclass
                           clus
vv                          AMP PEAK 14(8P11.21) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               49
                           clus
vv                          AMP PEAK 14(8P11.21) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED    1 40
  AMP PEAK 14(8P11.21) WILD-TYPE  5 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED      1   40
  AMP PEAK 14(8P11.21) WILD-TYPE    5   48
                        clus
vv                       AMP PEAK 14(8P11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 14(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             48
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8Q24.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(8Q24.21) MUTATED   83 62
  AMP PEAK 15(8Q24.21) WILD-TYPE 25 14
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           145                             39 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                            62                             14 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       60.39        34.85        18.28         4.31        24.00        19.99 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
        0.36        35.97        27.12        20.02        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78         2.63        20.12         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL 
        2.60         3.75        55.50        12.92        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        13.41        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       38.40        53.95        15.78         2.89        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        25.08        41.23         3.42         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T TCGA-Q9-A6FU TCGA-IG-A4P3 
       15.68         8.94         4.70        22.82         5.16        18.64 
TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A93E TCGA-KH-A6WC 
        9.30        23.41        14.86        47.38        25.22         6.28 
TCGA-L5-A4OF TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       26.33         7.17        29.00        15.48        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV 
        3.02         2.66        13.48        16.47        83.24        52.57 
TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6XQ 
       15.52         4.47        12.03        33.11         7.82         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA4G 
        9.30         2.30         3.42        25.81         1.55        18.05 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-AAPN 
       18.21        14.37         2.66 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.13                           1.55 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                         12.85                          14.37 
[1] "0.1 - 122.1 (12.8)" "1.6 - 83.2 (14.4)" 
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         6        2        5        1        35
  AMP PEAK 15(8Q24.21) WILD-TYPE       2        3        1        0        12
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          25        23         11          7
  AMP PEAK 15(8Q24.21) WILD-TYPE         6         2          3          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8Q24.21) MUTATED            7        4         3
  AMP PEAK 15(8Q24.21) WILD-TYPE          0        1         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               6                              2
  STAGE IA                              2                              3
  STAGE IB                              5                              1
  STAGE II                              1                              0
  STAGE IIA                            35                             12
  STAGE IIB                            25                              6
  STAGE III                            23                              2
  STAGE IIIA                           11                              3
  STAGE IIIB                            7                              2
  STAGE IIIC                            7                              0
  STAGE IV                              4                              1
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 15(8Q24.21) MUTATED      22 35 71  4
  AMP PEAK 15(8Q24.21) WILD-TYPE    10  8 16  1
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T0+T1                           22                             10
  T2                              35                              8
  T3                              71                             16
  T4                               4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 15(8Q24.21) MUTATED   58 57  8  8
  AMP PEAK 15(8Q24.21) WILD-TYPE 19 11  4  0
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           58                             19
  N1                           57                             11
  N2                            8                              4
  N3                            8                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   109   7
  AMP PEAK 15(8Q24.21) WILD-TYPE  26   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    109    7
  AMP PEAK 15(8Q24.21) WILD-TYPE   26    2
   clus
vv  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  0                          109                             26
  1                            7                              2
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED    16 129
  AMP PEAK 15(8Q24.21) WILD-TYPE  11  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED     16  129
  AMP PEAK 15(8Q24.21) WILD-TYPE   11   28
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                           16                             11
  MALE                            129                             28
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                              0  1
  AMP PEAK 15(8Q24.21) MUTATED   95 35
  AMP PEAK 15(8Q24.21) WILD-TYPE 28  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED     95   35
  AMP PEAK 15(8Q24.21) WILD-TYPE   28    8
     clus
vv    AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  NO                            95                             28
  YES                           35                              8
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, binary
                                cls
clus                              0  1
  AMP PEAK 15(8Q24.21) MUTATED   67 78
  AMP PEAK 15(8Q24.21) WILD-TYPE 21 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED     67   78
  AMP PEAK 15(8Q24.21) WILD-TYPE   21   18
                                   clus
vv                                  AMP PEAK 15(8Q24.21) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           78
                                   clus
vv                                  AMP PEAK 15(8Q24.21) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 21
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             18
[1] 2 2
[1] FALSE
D15V11, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(8Q24.21) MUTATED   112  11   1   4
  AMP PEAK 15(8Q24.21) WILD-TYPE  25   1   1   3
D15V12, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  R0                          112                             25
  R1                           11                              1
  R2                            1                              1
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q24.21) MUTATED      43                         3    82
  AMP PEAK 15(8Q24.21) WILD-TYPE     3                         2    32
D15V14, multiclass
                           clus
vv                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                               43
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               82
                           clus
vv                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                                cls
clus                              0  1
  AMP PEAK 15(8Q24.21) MUTATED    4 72
  AMP PEAK 15(8Q24.21) WILD-TYPE  2 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      4   72
  AMP PEAK 15(8Q24.21) WILD-TYPE    2   16
                        clus
vv                       AMP PEAK 15(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       AMP PEAK 15(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             16
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(9P13.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 16(9P13.3) MUTATED   22 18
  AMP PEAK 16(9P13.3) WILD-TYPE 86 58
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           40                           144 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           18                            58 
$`AMP PEAK 16(9P13.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GF 
       18.28         4.31         0.36        35.97        27.12        25.78 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43H 
       14.30         5.92        12.82       122.10        68.02         0.30 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NW 
       32.61        18.35         3.16        29.00        55.50        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A4MQ TCGA-LN-A7HY 
       10.36         5.92        13.41        12.33        12.33        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6KZ 
       13.18        12.33        13.38        12.85         7.82         5.06 
TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8EZ 
       16.31        15.78        20.38         9.27        22.82        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-A9VB 
       52.27         9.17        25.08         1.32 

$`AMP PEAK 16(9P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ 
       19.99        22.82         5.16        20.02        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25        26.33        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       10.85        10.45        12.66        12.43        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.00        12.23        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         8.02         7.59         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        46.19        18.05        11.24        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         2.66        19.73 

  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                         0.30                          0.13 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       13.395                        12.805 
[1] "0.3 - 122.1 (13.4)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.1"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P13.3) MUTATED         2        1        2        0         9
  AMP PEAK 16(9P13.3) WILD-TYPE       6        4        4        1        38
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P13.3) MUTATED           5         8          3          2
  AMP PEAK 16(9P13.3) WILD-TYPE        26        17         11          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(9P13.3) MUTATED            3        0         1
  AMP PEAK 16(9P13.3) WILD-TYPE          4        5         3
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                            9                            38
  STAGE IIB                            5                            26
  STAGE III                            8                            17
  STAGE IIIA                           3                            11
  STAGE IIIB                           2                             7
  STAGE IIIC                           3                             4
  STAGE IV                             0                             5
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 16(9P13.3) MUTATED       5  7 25  0
  AMP PEAK 16(9P13.3) WILD-TYPE    27 36 62  5
D16V4, multiclass
       clus
vv      AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  T0+T1                           5                            27
  T2                              7                            36
  T3                             25                            62
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 16(9P13.3) MUTATED   16 16  2  3
  AMP PEAK 16(9P13.3) WILD-TYPE 61 52 10  5
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  N0                          16                            61
  N1                          16                            52
  N2                           2                            10
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P13.3) MUTATED    29   1
  AMP PEAK 16(9P13.3) WILD-TYPE 106   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED     29    1
  AMP PEAK 16(9P13.3) WILD-TYPE  106    8
   clus
vv  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  0                          29                           106
  1                           1                             8
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P13.3) MUTATED     1  39
  AMP PEAK 16(9P13.3) WILD-TYPE  26 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      1   39
  AMP PEAK 16(9P13.3) WILD-TYPE   26  118
        clus
vv       AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  FEMALE                           1                            26
  MALE                            39                           118
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                             0  1
  AMP PEAK 16(9P13.3) MUTATED   27  9
  AMP PEAK 16(9P13.3) WILD-TYPE 96 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED     27    9
  AMP PEAK 16(9P13.3) WILD-TYPE   96   34
     clus
vv    AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  NO                           27                            96
  YES                           9                            34
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, binary
                               cls
clus                             0  1
  AMP PEAK 16(9P13.3) MUTATED   21 19
  AMP PEAK 16(9P13.3) WILD-TYPE 67 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED     21   19
  AMP PEAK 16(9P13.3) WILD-TYPE   67   77
                                   clus
vv                                  AMP PEAK 16(9P13.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              21
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          19
                                   clus
vv                                  AMP PEAK 16(9P13.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                67
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            77
[1] 2 2
[1] FALSE
D16V11, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(9P13.3) MUTATED    28   5   0   2
  AMP PEAK 16(9P13.3) WILD-TYPE 109   7   2   5
D16V12, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  R0                          28                           109
  R1                           5                             7
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(9P13.3) MUTATED      11                         1    24
  AMP PEAK 16(9P13.3) WILD-TYPE    35                         4    90
D16V14, multiclass
                           clus
vv                          AMP PEAK 16(9P13.3) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              24
                           clus
vv                          AMP PEAK 16(9P13.3) WILD-TYPE
  ASIAN                                                35
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                               cls
clus                             0  1
  AMP PEAK 16(9P13.3) MUTATED    1 18
  AMP PEAK 16(9P13.3) WILD-TYPE  5 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      1   18
  AMP PEAK 16(9P13.3) WILD-TYPE    5   70
                        clus
vv                       AMP PEAK 16(9P13.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK 16(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            70
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(9Q34.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 17(9Q34.3) MUTATED   45 19
  AMP PEAK 17(9Q34.3) WILD-TYPE 63 57
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           64                           120 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           19                            57 
$`AMP PEAK 17(9Q34.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GH 
       60.39         4.31         0.36        27.12        20.02        31.27 
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
        5.92         4.21         7.69         0.53        12.82         9.96 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C 
       14.50       122.10         3.68        47.38        23.18         3.16 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A891 
        3.32         1.38        29.00         7.13         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       55.50        13.22        13.41        46.09        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41        12.33        13.38        12.59        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.49        12.59        11.54        12.33         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR 
       10.52        12.00        13.18        13.38        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-VR-A8ER 
        8.02        16.31        53.95         2.30        20.38        12.43 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         1.32         2.66 

$`AMP PEAK 17(9Q34.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GI 
       19.99        22.82        35.97         5.16        25.78        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       58.55         7.63        13.94         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30        17.03         0.79        23.41 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86         4.67        12.16        44.75        68.02        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         3.16        58.59         4.90         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S 
       83.24        52.57        10.85        10.45        12.66        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35        13.25        12.46        12.59        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY 
       12.85        15.52        13.22        25.25        12.23        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.18         0.13        12.03        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7B 
       22.82         1.55        18.31         8.12        28.11        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        18.21        25.08         3.42         2.10        19.73 

  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                         0.36                          0.13 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       12.540                        13.515 
[1] "0.4 - 122.1 (12.5)" "0.1 - 83.2 (13.5)" 
[1] "hr=" "1.6"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9Q34.3) MUTATED         2        0        2        0        17
  AMP PEAK 17(9Q34.3) WILD-TYPE       6        5        4        1        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9Q34.3) MUTATED          14         9          6          2
  AMP PEAK 17(9Q34.3) WILD-TYPE        17        16          8          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(9Q34.3) MUTATED            4        1         0
  AMP PEAK 17(9Q34.3) WILD-TYPE          3        4         4
D17V3, multiclass
            clus
vv           AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           17                            30
  STAGE IIB                           14                            17
  STAGE III                            9                            16
  STAGE IIIA                           6                             8
  STAGE IIIB                           2                             7
  STAGE IIIC                           4                             3
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 17(9Q34.3) MUTATED       7 17 34  1
  AMP PEAK 17(9Q34.3) WILD-TYPE    25 26 53  4
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  T0+T1                           7                            25
  T2                             17                            26
  T3                             34                            53
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 17(9Q34.3) MUTATED   23 27  4  4
  AMP PEAK 17(9Q34.3) WILD-TYPE 54 41  8  4
D17V5, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  N0                          23                            54
  N1                          27                            41
  N2                           4                             8
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED   51  1
  AMP PEAK 17(9Q34.3) WILD-TYPE 84  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED     51    1
  AMP PEAK 17(9Q34.3) WILD-TYPE   84    8
   clus
vv  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  0                          51                            84
  1                           1                             8
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED    4 60
  AMP PEAK 17(9Q34.3) WILD-TYPE 23 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      4   60
  AMP PEAK 17(9Q34.3) WILD-TYPE   23   97
        clus
vv       AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                           4                            23
  MALE                            60                            97
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED   37 17
  AMP PEAK 17(9Q34.3) WILD-TYPE 86 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED     37   17
  AMP PEAK 17(9Q34.3) WILD-TYPE   86   26
     clus
vv    AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  NO                           37                            86
  YES                          17                            26
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED   28 36
  AMP PEAK 17(9Q34.3) WILD-TYPE 60 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED     28   36
  AMP PEAK 17(9Q34.3) WILD-TYPE   60   60
                                   clus
vv                                  AMP PEAK 17(9Q34.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              28
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          36
                                   clus
vv                                  AMP PEAK 17(9Q34.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                60
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            60
[1] 2 2
[1] FALSE
D17V11, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 17(9Q34.3) MUTATED   53  3  1  1
  AMP PEAK 17(9Q34.3) WILD-TYPE 84  9  1  6
D17V12, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  R0                          53                            84
  R1                           3                             9
  R2                           1                             1
  RX                           1                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9Q34.3) MUTATED      23                         1    34
  AMP PEAK 17(9Q34.3) WILD-TYPE    23                         4    80
D17V14, multiclass
                           clus
vv                          AMP PEAK 17(9Q34.3) MUTATED
  ASIAN                                              23
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              34
                           clus
vv                          AMP PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED    2 33
  AMP PEAK 17(9Q34.3) WILD-TYPE  4 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      2   33
  AMP PEAK 17(9Q34.3) WILD-TYPE    4   55
                        clus
vv                       AMP PEAK 17(9Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       AMP PEAK 17(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            55
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11P13) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 18(11P13) MUTATED   25 27
  AMP PEAK 18(11P13) WILD-TYPE 83 49
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          52                          132 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          27                           49 
$`AMP PEAK 18(11P13) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GK 
       18.28         8.94        24.00        27.12        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
        8.94        16.24         0.53        14.50       122.10         3.68 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT 
       25.22         6.28        32.61        47.93        18.35         4.90 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NN 
       29.00        15.48         3.75         2.66        13.48         5.49 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V 
       52.57        46.09         5.92        12.33        13.15        12.59 
TCGA-LN-A4A1 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HW TCGA-LN-A7HY 
       12.59        12.33        13.22         4.47        12.00        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        13.38        12.26         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ 
        7.04         6.35        53.95         7.00         3.42        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-ZR-A9CJ 
       12.43        18.31        18.18        19.73 

$`AMP PEAK 18(11P13) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27        14.30         5.92        13.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        24.03         3.16        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.13         7.43         2.60        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37         8.71        13.41        83.24        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39        12.85        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       10.52        12.23        13.18        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 
       12.85        33.11         5.06        16.31        38.40         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 

  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                        0.53                         0.13 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                       12.51                        13.20 
[1] "0.5 - 122.1 (12.5)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.4"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(11P13) MUTATED         3        2        2        0        12
  AMP PEAK 18(11P13) WILD-TYPE       5        3        4        1        35
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(11P13) MUTATED           4         9          3          2
  AMP PEAK 18(11P13) WILD-TYPE        27        16         11          7
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(11P13) MUTATED            2        3         2
  AMP PEAK 18(11P13) WILD-TYPE          5        2         2
D18V3, multiclass
            clus
vv           AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            2                            3
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          12                           35
  STAGE IIB                           4                           27
  STAGE III                           9                           16
  STAGE IIIA                          3                           11
  STAGE IIIB                          2                            7
  STAGE IIIC                          2                            5
  STAGE IV                            3                            2
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 18(11P13) MUTATED       9  6 30  1
  AMP PEAK 18(11P13) WILD-TYPE    23 37 57  4
D18V4, multiclass
       clus
vv      AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  T0+T1                          9                           23
  T2                             6                           37
  T3                            30                           57
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 18(11P13) MUTATED   19 21  3  2
  AMP PEAK 18(11P13) WILD-TYPE 58 47  9  6
D18V5, multiclass
    clus
vv   AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  N0                         19                           58
  N1                         21                           47
  N2                          3                            9
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                              cls
clus                             0   1
  AMP PEAK 18(11P13) MUTATED    34   5
  AMP PEAK 18(11P13) WILD-TYPE 101   4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED     34    5
  AMP PEAK 18(11P13) WILD-TYPE  101    4
   clus
vv  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  0                         34                          101
  1                          5                            4
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(11P13) MUTATED     4  48
  AMP PEAK 18(11P13) WILD-TYPE  23 109
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED      4   48
  AMP PEAK 18(11P13) WILD-TYPE   23  109
        clus
vv       AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  FEMALE                          4                           23
  MALE                           48                          109
[1] 2 2
[1] FALSE
D18V8, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED   34 12
  AMP PEAK 18(11P13) WILD-TYPE 89 31
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED     34   12
  AMP PEAK 18(11P13) WILD-TYPE   89   31
     clus
vv    AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  NO                          34                           89
  YES                         12                           31
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED   29 23
  AMP PEAK 18(11P13) WILD-TYPE 59 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED     29   23
  AMP PEAK 18(11P13) WILD-TYPE   59   73
                                   clus
vv                                  AMP PEAK 18(11P13) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             29
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         23
                                   clus
vv                                  AMP PEAK 18(11P13) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               59
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           73
[1] 2 2
[1] FALSE
D18V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(11P13) MUTATED    34   5   1   3
  AMP PEAK 18(11P13) WILD-TYPE 103   7   1   4
D18V12, multiclass
    clus
vv   AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  R0                         34                          103
  R1                          5                            7
  R2                          1                            1
  RX                          3                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11P13) MUTATED      15                         1    30
  AMP PEAK 18(11P13) WILD-TYPE    31                         4    84
D18V14, multiclass
                           clus
vv                          AMP PEAK 18(11P13) MUTATED
  ASIAN                                             15
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             30
                           clus
vv                          AMP PEAK 18(11P13) WILD-TYPE
  ASIAN                                               31
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED    0 25
  AMP PEAK 18(11P13) WILD-TYPE  6 63
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED      0   25
  AMP PEAK 18(11P13) WILD-TYPE    6   63
                        clus
vv                       AMP PEAK 18(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         25
                        clus
vv                       AMP PEAK 18(11P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(11P13) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 19(11P13) MUTATED   24 26
  AMP PEAK 19(11P13) WILD-TYPE 84 50
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          50                          134 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          26                           50 
$`AMP PEAK 19(11P13) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-2H-A9GK TCGA-2H-A9GN 
       18.28         8.94        24.00        27.12         7.63         8.94 
TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
       16.24         0.53         4.67        14.50       122.10         3.68 
TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU 
       25.22        32.61        47.93        18.35         4.90        29.00 
TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       15.48         2.66         5.49        52.57        46.09         5.92 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       12.33        13.15        12.59        12.59        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ 
       13.22         4.47        10.52        12.00        12.03        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       13.38        12.85        12.26         7.82         7.59         7.04 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX 
        7.00         3.42        22.82        12.43        18.31        28.11 
TCGA-VR-A8EZ TCGA-ZR-A9CJ 
       18.18        19.73 

$`AMP PEAK 19(11P13) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       31.27        14.30        58.55         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.79        23.41        12.82         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       26.33        21.01         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       58.59         7.13         7.43         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        55.50        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        13.38        15.35        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.33        25.25        12.23        13.18        13.18         0.13 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.03        33.11         8.02         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       12.69        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY 
        8.98        25.81        27.09         1.55         8.12        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                        0.53                         0.13 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                       12.59                        13.20 
[1] "0.5 - 122.1 (12.6)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.5"
D19V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(11P13) MUTATED         2        1        2        0        15
  AMP PEAK 19(11P13) WILD-TYPE       6        4        4        1        32
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(11P13) MUTATED           4         8          3          3
  AMP PEAK 19(11P13) WILD-TYPE        27        17         11          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(11P13) MUTATED            2        3         3
  AMP PEAK 19(11P13) WILD-TYPE          5        2         1
D19V3, multiclass
            clus
vv           AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            4
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          15                           32
  STAGE IIB                           4                           27
  STAGE III                           8                           17
  STAGE IIIA                          3                           11
  STAGE IIIB                          3                            6
  STAGE IIIC                          2                            5
  STAGE IV                            3                            2
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 19(11P13) MUTATED       8  8 30  1
  AMP PEAK 19(11P13) WILD-TYPE    24 35 57  4
D19V4, multiclass
       clus
vv      AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  T0+T1                          8                           24
  T2                             8                           35
  T3                            30                           57
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 19(11P13) MUTATED   20 20  4  2
  AMP PEAK 19(11P13) WILD-TYPE 57 48  8  6
D19V5, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  N0                         20                           57
  N1                         20                           48
  N2                          4                            8
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                              cls
clus                             0   1
  AMP PEAK 19(11P13) MUTATED    34   6
  AMP PEAK 19(11P13) WILD-TYPE 101   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED     34    6
  AMP PEAK 19(11P13) WILD-TYPE  101    3
   clus
vv  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  0                         34                          101
  1                          6                            3
[1] 2 2
[1] FALSE
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(11P13) MUTATED     4  46
  AMP PEAK 19(11P13) WILD-TYPE  23 111
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      4   46
  AMP PEAK 19(11P13) WILD-TYPE   23  111
        clus
vv       AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  FEMALE                          4                           23
  MALE                           46                          111
[1] 2 2
[1] FALSE
D19V8, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED   33 12
  AMP PEAK 19(11P13) WILD-TYPE 90 31
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED     33   12
  AMP PEAK 19(11P13) WILD-TYPE   90   31
     clus
vv    AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  NO                          33                           90
  YES                         12                           31
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED   23 27
  AMP PEAK 19(11P13) WILD-TYPE 65 69
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED     23   27
  AMP PEAK 19(11P13) WILD-TYPE   65   69
                                   clus
vv                                  AMP PEAK 19(11P13) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         27
                                   clus
vv                                  AMP PEAK 19(11P13) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           69
[1] 2 2
[1] FALSE
D19V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 19(11P13) MUTATED    36   5   1   3
  AMP PEAK 19(11P13) WILD-TYPE 101   7   1   4
D19V12, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  R0                         36                          101
  R1                          5                            7
  R2                          1                            1
  RX                          3                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(11P13) MUTATED      19                         1    24
  AMP PEAK 19(11P13) WILD-TYPE    27                         4    90
D19V14, multiclass
                           clus
vv                          AMP PEAK 19(11P13) MUTATED
  ASIAN                                             19
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             24
                           clus
vv                          AMP PEAK 19(11P13) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED    0 25
  AMP PEAK 19(11P13) WILD-TYPE  6 63
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      0   25
  AMP PEAK 19(11P13) WILD-TYPE    6   63
                        clus
vv                       AMP PEAK 19(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         25
                        clus
vv                       AMP PEAK 19(11P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(11Q13.3) MUTATED   64 40
  AMP PEAK 20(11Q13.3) WILD-TYPE 44 36
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           104                             80 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            40                             36 
$`AMP PEAK 20(11Q13.3) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88Y TCGA-2H-A9GN TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.70         0.36         8.94        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
       20.12        18.64        17.03        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43H 
       14.50        12.16       122.10         3.68        25.22         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       26.33        32.61        47.93         1.38        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV 
       13.48        13.55         5.49        21.37         8.71        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       46.09        10.85         5.92        12.66        12.43        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22        12.33        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
       12.26         7.82         8.02         7.59         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
       53.95        15.78         7.00         3.42         9.27        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`AMP PEAK 20(11Q13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       15.68        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       35.21         2.63         3.88         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.82        14.86        44.75        68.02        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       30.25        21.01        18.35         3.32         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        4.90         7.13         7.43        25.12         7.40         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         7.76        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A4A9 TCGA-LN-A5U5 
       10.45        13.41        12.33        15.35        11.54         4.47 
TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 
       10.52        13.38        12.85        33.11         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       38.40         9.30         2.89         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET 
        5.29        16.44        15.35         8.98        27.09         1.55 
TCGA-VR-A8Q7 TCGA-X8-AAAR 
       52.27        18.21 

  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          0.13                           0.53 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                         12.71                          13.41 
[1] "0.1 - 122.1 (12.7)" "0.5 - 83.2 (13.4)" 
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(11Q13.3) MUTATED         4        1        2        1        30
  AMP PEAK 20(11Q13.3) WILD-TYPE       4        4        4        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(11Q13.3) MUTATED          17        16          9          4
  AMP PEAK 20(11Q13.3) WILD-TYPE        14         9          5          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(11Q13.3) MUTATED            3        3         3
  AMP PEAK 20(11Q13.3) WILD-TYPE          4        2         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            30                             17
  STAGE IIB                            17                             14
  STAGE III                            16                              9
  STAGE IIIA                            9                              5
  STAGE IIIB                            4                              5
  STAGE IIIC                            3                              4
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 20(11Q13.3) MUTATED      15 27 50  4
  AMP PEAK 20(11Q13.3) WILD-TYPE    17 16 37  1
D20V4, multiclass
       clus
vv      AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  T0+T1                           15                             17
  T2                              27                             16
  T3                              50                             37
  T4                               4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 20(11Q13.3) MUTATED   46 38  7  4
  AMP PEAK 20(11Q13.3) WILD-TYPE 31 30  5  4
D20V5, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  N0                           46                             31
  N1                           38                             30
  N2                            7                              5
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   79  6
  AMP PEAK 20(11Q13.3) WILD-TYPE 56  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     79    6
  AMP PEAK 20(11Q13.3) WILD-TYPE   56    3
   clus
vv  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  0                           79                             56
  1                            6                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   16 88
  AMP PEAK 20(11Q13.3) WILD-TYPE 11 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     16   88
  AMP PEAK 20(11Q13.3) WILD-TYPE   11   69
        clus
vv       AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  FEMALE                           16                             11
  MALE                             88                             69
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   67 28
  AMP PEAK 20(11Q13.3) WILD-TYPE 56 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     67   28
  AMP PEAK 20(11Q13.3) WILD-TYPE   56   15
     clus
vv    AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  NO                            67                             56
  YES                           28                             15
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   37 67
  AMP PEAK 20(11Q13.3) WILD-TYPE 51 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     37   67
  AMP PEAK 20(11Q13.3) WILD-TYPE   51   29
                                   clus
vv                                  AMP PEAK 20(11Q13.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               37
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           67
                                   clus
vv                                  AMP PEAK 20(11Q13.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 51
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             29
[1] 2 2
[1] FALSE
D20V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(11Q13.3) MUTATED   77  5  1  6
  AMP PEAK 20(11Q13.3) WILD-TYPE 60  7  1  1
D20V12, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  R0                           77                             60
  R1                            5                              7
  R2                            1                              1
  RX                            6                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q13.3) MUTATED      32                         4    62
  AMP PEAK 20(11Q13.3) WILD-TYPE    14                         1    52
D20V14, multiclass
                           clus
vv                          AMP PEAK 20(11Q13.3) MUTATED
  ASIAN                                               32
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               62
                           clus
vv                          AMP PEAK 20(11Q13.3) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED    3 55
  AMP PEAK 20(11Q13.3) WILD-TYPE  3 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED      3   55
  AMP PEAK 20(11Q13.3) WILD-TYPE    3   33
                        clus
vv                       AMP PEAK 20(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       AMP PEAK 20(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             33
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(12P12.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(12P12.1) MUTATED   47 32
  AMP PEAK 21(12P12.1) WILD-TYPE 61 44
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            79                            105 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            32                             44 
$`AMP PEAK 21(12P12.1) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV 
        4.31        24.00        19.99         0.36        27.12        20.02 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         5.92        16.24         4.21        32.45        35.21 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 
        2.63        20.12        18.64         3.88         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A93D TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       14.50        31.56         0.30        47.93        18.35         3.32 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        4.90        29.00        15.48         2.66        16.47        13.22 
TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       21.37        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       12.66        13.41        12.33        13.38        13.15        12.59 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       13.25        12.59        12.76        12.59        12.85        15.52 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        12.33        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW 
        5.06        38.40         6.35        53.95        12.69        20.38 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       27.09         1.55        18.31         8.12        28.11        18.18 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`AMP PEAK 21(12P12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       22.82        35.97         5.16        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       58.55        13.94         8.94         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
       21.01         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49U 
        8.71        13.41        83.24        52.57        12.43        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.62        12.46        12.49        22.39        11.54        12.33 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.23        12.03        13.38        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       33.11         7.82        16.31         7.04         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       15.91        25.08        41.23 

  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                          0.13                           0.79 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                         12.85                          13.38 
[1] "0.1 - 54.0 (12.8)"  "0.8 - 122.1 (13.4)"
[1] "hr=" "1.3"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(12P12.1) MUTATED         0        1        3        1        24
  AMP PEAK 21(12P12.1) WILD-TYPE       8        4        3        0        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(12P12.1) MUTATED           8        10          6          4
  AMP PEAK 21(12P12.1) WILD-TYPE        23        15          8          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(12P12.1) MUTATED            6        3         3
  AMP PEAK 21(12P12.1) WILD-TYPE          1        2         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  STAGE I                               0                              8
  STAGE IA                              1                              4
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            24                             23
  STAGE IIB                             8                             23
  STAGE III                            10                             15
  STAGE IIIA                            6                              8
  STAGE IIIB                            4                              5
  STAGE IIIC                            6                              1
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 21(12P12.1) MUTATED       8 20 43  0
  AMP PEAK 21(12P12.1) WILD-TYPE    24 23 44  5
D21V4, multiclass
       clus
vv      AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  T0+T1                            8                             24
  T2                              20                             23
  T3                              43                             44
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 21(12P12.1) MUTATED   33 27  4  6
  AMP PEAK 21(12P12.1) WILD-TYPE 44 41  8  2
D21V5, multiclass
    clus
vv   AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  N0                           33                             44
  N1                           27                             41
  N2                            4                              8
  N3                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED   53  6
  AMP PEAK 21(12P12.1) WILD-TYPE 82  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED     53    6
  AMP PEAK 21(12P12.1) WILD-TYPE   82    3
   clus
vv  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  0                           53                             82
  1                            6                              3
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED    4 75
  AMP PEAK 21(12P12.1) WILD-TYPE 23 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED      4   75
  AMP PEAK 21(12P12.1) WILD-TYPE   23   82
        clus
vv       AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  FEMALE                            4                             23
  MALE                             75                             82
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED   48 22
  AMP PEAK 21(12P12.1) WILD-TYPE 75 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED     48   22
  AMP PEAK 21(12P12.1) WILD-TYPE   75   21
     clus
vv    AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  NO                            48                             75
  YES                           22                             21
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED   30 49
  AMP PEAK 21(12P12.1) WILD-TYPE 58 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED     30   49
  AMP PEAK 21(12P12.1) WILD-TYPE   58   47
                                   clus
vv                                  AMP PEAK 21(12P12.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           49
                                   clus
vv                                  AMP PEAK 21(12P12.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             47
[1] 2 2
[1] FALSE
D21V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 21(12P12.1) MUTATED   56  6  1  3
  AMP PEAK 21(12P12.1) WILD-TYPE 81  6  1  4
D21V12, multiclass
    clus
vv   AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  R0                           56                             81
  R1                            6                              6
  R2                            1                              1
  RX                            3                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(12P12.1) MUTATED      27                         2    44
  AMP PEAK 21(12P12.1) WILD-TYPE    19                         3    70
D21V14, multiclass
                           clus
vv                          AMP PEAK 21(12P12.1) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               44
                           clus
vv                          AMP PEAK 21(12P12.1) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED    2 47
  AMP PEAK 21(12P12.1) WILD-TYPE  4 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED      2   47
  AMP PEAK 21(12P12.1) WILD-TYPE    4   41
                        clus
vv                       AMP PEAK 21(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       AMP PEAK 21(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             41
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(12Q15) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 22(12Q15) MUTATED   28 23
  AMP PEAK 22(12Q15) WILD-TYPE 80 53
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          51                          133 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          23                           53 
$`AMP PEAK 22(12Q15) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-2H-A9GK TCGA-2H-A9GO 
        4.31         8.94        24.00        27.12         7.63        16.24 
TCGA-2H-A9GR TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
       32.45         0.53         4.67        21.01        47.93         3.32 
TCGA-L5-A4OT TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL 
        4.90        15.48        55.50         2.66        13.48        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V 
        5.49        52.57        46.09        10.36        10.45        12.59 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.25        12.59        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR 
       12.33         4.47        12.33        13.18         0.13        12.26 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
        7.59        38.40         6.35        12.69        20.38         3.42 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
       27.09         1.55        28.11        18.18        52.27        11.24 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.21         2.10        19.73 

$`AMP PEAK 22(12Q15) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        12.92        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        83.24        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MR 
       12.62        12.46        12.49        12.76        22.39        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        13.38        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        16.31         7.04        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         2.30         7.00         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       18.31         8.12        33.70        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        0.13                         0.30 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        55.5                        122.1 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                       12.59                        13.22 
[1] "0.1 - 55.5 (12.6)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.2"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(12Q15) MUTATED         1        1        3        1        11
  AMP PEAK 22(12Q15) WILD-TYPE       7        4        3        0        36
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(12Q15) MUTATED           4         7          3          3
  AMP PEAK 22(12Q15) WILD-TYPE        27        18         11          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(12Q15) MUTATED            4        3         3
  AMP PEAK 22(12Q15) WILD-TYPE          3        2         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            1                            4
  STAGE IB                            3                            3
  STAGE II                            1                            0
  STAGE IIA                          11                           36
  STAGE IIB                           4                           27
  STAGE III                           7                           18
  STAGE IIIA                          3                           11
  STAGE IIIB                          3                            6
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 22(12Q15) MUTATED       5 12 29  0
  AMP PEAK 22(12Q15) WILD-TYPE    27 31 58  5
D22V4, multiclass
       clus
vv      AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  T0+T1                          5                           27
  T2                            12                           31
  T3                            29                           58
  T4                             0                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 22(12Q15) MUTATED   19 18  4  5
  AMP PEAK 22(12Q15) WILD-TYPE 58 50  8  3
D22V5, multiclass
    clus
vv   AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  N0                         19                           58
  N1                         18                           50
  N2                          4                            8
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                              cls
clus                             0   1
  AMP PEAK 22(12Q15) MUTATED    31   6
  AMP PEAK 22(12Q15) WILD-TYPE 104   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED     31    6
  AMP PEAK 22(12Q15) WILD-TYPE  104    3
   clus
vv  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  0                         31                          104
  1                          6                            3
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(12Q15) MUTATED     6  45
  AMP PEAK 22(12Q15) WILD-TYPE  21 112
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED      6   45
  AMP PEAK 22(12Q15) WILD-TYPE   21  112
        clus
vv       AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  FEMALE                          6                           21
  MALE                           45                          112
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                            0  1
  AMP PEAK 22(12Q15) MUTATED   35 10
  AMP PEAK 22(12Q15) WILD-TYPE 88 33
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED     35   10
  AMP PEAK 22(12Q15) WILD-TYPE   88   33
     clus
vv    AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  NO                          35                           88
  YES                         10                           33
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, binary
                              cls
clus                            0  1
  AMP PEAK 22(12Q15) MUTATED   23 28
  AMP PEAK 22(12Q15) WILD-TYPE 65 68
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED     23   28
  AMP PEAK 22(12Q15) WILD-TYPE   65   68
                                   clus
vv                                  AMP PEAK 22(12Q15) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         28
                                   clus
vv                                  AMP PEAK 22(12Q15) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           68
[1] 2 2
[1] FALSE
D22V11, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(12Q15) MUTATED    33   4   1   4
  AMP PEAK 22(12Q15) WILD-TYPE 104   8   1   3
D22V12, multiclass
    clus
vv   AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  R0                         33                          104
  R1                          4                            8
  R2                          1                            1
  RX                          4                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(12Q15) MUTATED      16                         1    29
  AMP PEAK 22(12Q15) WILD-TYPE    30                         4    85
D22V14, multiclass
                           clus
vv                          AMP PEAK 22(12Q15) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             29
                           clus
vv                          AMP PEAK 22(12Q15) WILD-TYPE
  ASIAN                                               30
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                              cls
clus                            0  1
  AMP PEAK 22(12Q15) MUTATED    1 24
  AMP PEAK 22(12Q15) WILD-TYPE  5 64
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED      1   24
  AMP PEAK 22(12Q15) WILD-TYPE    5   64
                        clus
vv                       AMP PEAK 22(12Q15) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         24
                        clus
vv                       AMP PEAK 22(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           64
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(13Q22.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(13Q22.1) MUTATED   39 26
  AMP PEAK 23(13Q22.1) WILD-TYPE 69 50
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            65                            119 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            26                             50 
$`AMP PEAK 23(13Q22.1) MUTATED`
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV 
        8.94         4.70        19.99         0.36        27.12        20.02 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30         5.92        13.94         4.21         7.69 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH 
        0.53         0.79        14.50       122.10         3.68        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OP TCGA-L5-A4OQ 
       23.18        31.56         3.16        30.25         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       58.59         7.13        15.48         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49L 
       12.92        13.55         8.71        13.41        46.09        10.45 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.38        15.35        12.59        12.59        12.59        12.85 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FQ TCGA-Q9-A6FW 
       12.33        25.25        12.00        12.23        12.85         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EZ 
       15.78        12.69         5.29         3.42         9.27        18.18 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-ZR-A9CJ 
       46.19        18.21        25.08        14.37        19.73 

$`AMP PEAK 23(13Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
       22.82        35.97         5.16        25.78        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93E 
       12.16        44.75        68.02        41.52        21.70        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         6.28         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93        18.35         3.32         3.16         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NI 
        7.43         2.60        25.12         7.40         3.75        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       16.47        13.22         7.76         5.49        21.37        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.85        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        12.33        13.15        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.49        12.76        22.39        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        12.33        10.52        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.03        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.59         5.06         6.35         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23         3.42         2.10         1.32         2.66 

  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                          0.36                           0.13 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                         12.85                          13.18 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1"  
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(13Q22.1) MUTATED         4        1        3        1        10
  AMP PEAK 23(13Q22.1) WILD-TYPE       4        4        3        0        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(13Q22.1) MUTATED          12         8          3          2
  AMP PEAK 23(13Q22.1) WILD-TYPE        19        17         11          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(13Q22.1) MUTATED            4        1         2
  AMP PEAK 23(13Q22.1) WILD-TYPE          3        4         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            10                             37
  STAGE IIB                            12                             19
  STAGE III                             8                             17
  STAGE IIIA                            3                             11
  STAGE IIIB                            2                              7
  STAGE IIIC                            4                              3
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 23(13Q22.1) MUTATED      15 13 27  0
  AMP PEAK 23(13Q22.1) WILD-TYPE    17 30 60  5
D23V4, multiclass
       clus
vv      AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  T0+T1                           15                             17
  T2                              13                             30
  T3                              27                             60
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 23(13Q22.1) MUTATED   22 24  4  4
  AMP PEAK 23(13Q22.1) WILD-TYPE 55 44  8  4
D23V5, multiclass
    clus
vv   AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  N0                           22                             55
  N1                           24                             44
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED   42  3
  AMP PEAK 23(13Q22.1) WILD-TYPE 93  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED     42    3
  AMP PEAK 23(13Q22.1) WILD-TYPE   93    6
   clus
vv  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  0                           42                             93
  1                            3                              6
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(13Q22.1) MUTATED     8  57
  AMP PEAK 23(13Q22.1) WILD-TYPE  19 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED      8   57
  AMP PEAK 23(13Q22.1) WILD-TYPE   19  100
        clus
vv       AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  FEMALE                            8                             19
  MALE                             57                            100
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED   45 13
  AMP PEAK 23(13Q22.1) WILD-TYPE 78 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED     45   13
  AMP PEAK 23(13Q22.1) WILD-TYPE   78   30
     clus
vv    AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  NO                            45                             78
  YES                           13                             30
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED   43 22
  AMP PEAK 23(13Q22.1) WILD-TYPE 45 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED     43   22
  AMP PEAK 23(13Q22.1) WILD-TYPE   45   74
                                   clus
vv                                  AMP PEAK 23(13Q22.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               43
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           22
                                   clus
vv                                  AMP PEAK 23(13Q22.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 45
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D23V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 23(13Q22.1) MUTATED   46  3  0  2
  AMP PEAK 23(13Q22.1) WILD-TYPE 91  9  2  5
D23V12, multiclass
    clus
vv   AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  R0                           46                             91
  R1                            3                              9
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(13Q22.1) MUTATED      15                         3    38
  AMP PEAK 23(13Q22.1) WILD-TYPE    31                         2    76
D23V14, multiclass
                           clus
vv                          AMP PEAK 23(13Q22.1) MUTATED
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               38
                           clus
vv                          AMP PEAK 23(13Q22.1) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED    5 28
  AMP PEAK 23(13Q22.1) WILD-TYPE  1 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED      5   28
  AMP PEAK 23(13Q22.1) WILD-TYPE    1   60
                        clus
vv                       AMP PEAK 23(13Q22.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK 23(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             60
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(14Q21.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 24(14Q21.1) MUTATED   36 25
  AMP PEAK 24(14Q21.1) WILD-TYPE 72 51
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            61                            123 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            25                             51 
$`AMP PEAK 24(14Q21.1) MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GR 
        4.31        35.97        20.02        25.78         5.92        32.45 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A8O2 
        0.85        20.78        18.64         0.53         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OR 
       12.16        47.38        23.18         3.16        30.25         3.16 
TCGA-L5-A4OX TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L 
        7.43         5.49        21.37        13.41         5.92        10.45 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.41        13.15        15.35        12.59        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY 
       22.39        11.54        13.22        12.33        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.18        12.33         0.13        12.03        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-AASX TCGA-VR-A8ER 
        8.02        38.40        53.95        20.38         8.98        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
        8.12        28.11        18.18        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       15.91        25.08        14.37         3.42         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

$`AMP PEAK 24(14Q21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB 
       16.24         4.21         7.69        33.27        35.21         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12         3.88         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       12.82        14.86        14.50       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.55        13.22         7.76         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.85        10.36        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       12.33        13.38        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.76        12.85        15.52        12.33         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-Q9-A6FW 
       10.52        12.00        13.38        13.18        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        16.31         7.04         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
       22.82         1.55        18.31        33.70        52.27        18.05 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-AAPN 
       18.21        41.23         2.66 

  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                          0.13                           0.30 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                         12.59                          13.38 
[1] "0.1 - 54.0 (12.6)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.2"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(14Q21.1) MUTATED         1        1        1        0        19
  AMP PEAK 24(14Q21.1) WILD-TYPE       7        4        5        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(14Q21.1) MUTATED          12         8          6          3
  AMP PEAK 24(14Q21.1) WILD-TYPE        19        17          8          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(14Q21.1) MUTATED            3        1         1
  AMP PEAK 24(14Q21.1) WILD-TYPE          4        4         3
D24V3, multiclass
            clus
vv           AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              4
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                            19                             28
  STAGE IIB                            12                             19
  STAGE III                             8                             17
  STAGE IIIA                            6                              8
  STAGE IIIB                            3                              6
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 24(14Q21.1) MUTATED       5 19 28  4
  AMP PEAK 24(14Q21.1) WILD-TYPE    27 24 59  1
D24V4, multiclass
       clus
vv      AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  T0+T1                            5                             27
  T2                              19                             24
  T3                              28                             59
  T4                               4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 24(14Q21.1) MUTATED   28 21  3  4
  AMP PEAK 24(14Q21.1) WILD-TYPE 49 47  9  4
D24V5, multiclass
    clus
vv   AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  N0                           28                             49
  N1                           21                             47
  N2                            3                              9
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED   49  2
  AMP PEAK 24(14Q21.1) WILD-TYPE 86  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED     49    2
  AMP PEAK 24(14Q21.1) WILD-TYPE   86    7
   clus
vv  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  0                           49                             86
  1                            2                              7
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED    2 59
  AMP PEAK 24(14Q21.1) WILD-TYPE 25 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED      2   59
  AMP PEAK 24(14Q21.1) WILD-TYPE   25   98
        clus
vv       AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  FEMALE                            2                             25
  MALE                             59                             98
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED   38 18
  AMP PEAK 24(14Q21.1) WILD-TYPE 85 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED     38   18
  AMP PEAK 24(14Q21.1) WILD-TYPE   85   25
     clus
vv    AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  NO                            38                             85
  YES                           18                             25
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED   19 42
  AMP PEAK 24(14Q21.1) WILD-TYPE 69 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED     19   42
  AMP PEAK 24(14Q21.1) WILD-TYPE   69   54
                                   clus
vv                                  AMP PEAK 24(14Q21.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               19
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           42
                                   clus
vv                                  AMP PEAK 24(14Q21.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             54
[1] 2 2
[1] FALSE
D24V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 24(14Q21.1) MUTATED   47  4  1  2
  AMP PEAK 24(14Q21.1) WILD-TYPE 90  8  1  5
D24V12, multiclass
    clus
vv   AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  R0                           47                             90
  R1                            4                              8
  R2                            1                              1
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(14Q21.1) MUTATED      24                         2    29
  AMP PEAK 24(14Q21.1) WILD-TYPE    22                         3    85
D24V14, multiclass
                           clus
vv                          AMP PEAK 24(14Q21.1) MUTATED
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               29
                           clus
vv                          AMP PEAK 24(14Q21.1) WILD-TYPE
  ASIAN                                                 22
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED    2 37
  AMP PEAK 24(14Q21.1) WILD-TYPE  4 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED      2   37
  AMP PEAK 24(14Q21.1) WILD-TYPE    4   51
                        clus
vv                       AMP PEAK 24(14Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       AMP PEAK 24(14Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             51
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(15Q26.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 25(15Q26.1) MUTATED   30 28
  AMP PEAK 25(15Q26.1) WILD-TYPE 78 48
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            58                            126 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            28                             48 
$`AMP PEAK 25(15Q26.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A88Y TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
       60.39         8.94         0.36        25.78        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH 
        8.94        32.45         0.53       122.10         3.68        47.38 
TCGA-L5-A43C TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        3.16        47.93         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        4.90        29.00         7.13        15.48         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G 
       55.50        16.47        21.37        13.41        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV 
       10.36        10.45        13.38        22.39        13.22        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.00        12.23        12.33        33.11         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-AA7B 
       20.38        27.09        22.82         1.55        18.31        11.24 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-ZR-A9CJ 
        9.17        25.08        41.23        19.73 

$`AMP PEAK 25(15Q26.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       12.16        44.75        68.02        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OX 
       26.33        32.61        21.01        18.35         3.32         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49         8.71        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       52.57         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY 
       11.54        12.33         4.47        12.33        25.25        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WC 
       12.26         8.02         5.06        38.40         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27         8.98        25.81        12.43         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I 
       33.70        18.18        52.27        46.19        18.05        15.91 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        14.37         3.42         2.10         1.32         2.66 

  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                          0.36                           0.13 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                        12.775                         13.035 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.0)" 
[1] "hr=" "1"  
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(15Q26.1) MUTATED         3        3        3        0        13
  AMP PEAK 25(15Q26.1) WILD-TYPE       5        2        3        1        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(15Q26.1) MUTATED           6         8          2          2
  AMP PEAK 25(15Q26.1) WILD-TYPE        25        17         12          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(15Q26.1) MUTATED            3        3         1
  AMP PEAK 25(15Q26.1) WILD-TYPE          4        2         3
D25V3, multiclass
            clus
vv           AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              3                              2
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                            13                             34
  STAGE IIB                             6                             25
  STAGE III                             8                             17
  STAGE IIIA                            2                             12
  STAGE IIIB                            2                              7
  STAGE IIIC                            3                              4
  STAGE IV                              3                              2
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 25(15Q26.1) MUTATED       8 18 24  0
  AMP PEAK 25(15Q26.1) WILD-TYPE    24 25 63  5
D25V4, multiclass
       clus
vv      AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  T0+T1                            8                             24
  T2                              18                             25
  T3                              24                             63
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 25(15Q26.1) MUTATED   23 19  4  4
  AMP PEAK 25(15Q26.1) WILD-TYPE 54 49  8  4
D25V5, multiclass
    clus
vv   AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  N0                           23                             54
  N1                           19                             49
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(15Q26.1) MUTATED    35   4
  AMP PEAK 25(15Q26.1) WILD-TYPE 100   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED     35    4
  AMP PEAK 25(15Q26.1) WILD-TYPE  100    5
   clus
vv  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  0                           35                            100
  1                            4                              5
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(15Q26.1) MUTATED     8  50
  AMP PEAK 25(15Q26.1) WILD-TYPE  19 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED      8   50
  AMP PEAK 25(15Q26.1) WILD-TYPE   19  107
        clus
vv       AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  FEMALE                            8                             19
  MALE                             50                            107
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED   42 11
  AMP PEAK 25(15Q26.1) WILD-TYPE 81 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED     42   11
  AMP PEAK 25(15Q26.1) WILD-TYPE   81   32
     clus
vv    AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  NO                            42                             81
  YES                           11                             32
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED   36 22
  AMP PEAK 25(15Q26.1) WILD-TYPE 52 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED     36   22
  AMP PEAK 25(15Q26.1) WILD-TYPE   52   74
                                   clus
vv                                  AMP PEAK 25(15Q26.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               36
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           22
                                   clus
vv                                  AMP PEAK 25(15Q26.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 52
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D25V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 25(15Q26.1) MUTATED   45  3  0  2
  AMP PEAK 25(15Q26.1) WILD-TYPE 92  9  2  5
D25V12, multiclass
    clus
vv   AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  R0                           45                             92
  R1                            3                              9
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(15Q26.1) MUTATED       9                         2    38
  AMP PEAK 25(15Q26.1) WILD-TYPE    37                         3    76
D25V14, multiclass
                           clus
vv                          AMP PEAK 25(15Q26.1) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               38
                           clus
vv                          AMP PEAK 25(15Q26.1) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED    3 20
  AMP PEAK 25(15Q26.1) WILD-TYPE  3 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED      3   20
  AMP PEAK 25(15Q26.1) WILD-TYPE    3   68
                        clus
vv                       AMP PEAK 25(15Q26.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 25(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             68
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(17Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 26(17Q12) MUTATED   44 31
  AMP PEAK 26(17Q12) WILD-TYPE 64 45
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          75                          109 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          31                           45 
$`AMP PEAK 26(17Q12) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        34.85        18.28        24.00        35.97        27.12 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         8.94         7.69 
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A93C TCGA-JY-A93D 
       35.21         0.53        17.03        12.82        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       25.22        30.25         0.30        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z 
       58.59         4.90        29.00         7.13         2.60         7.40 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        13.48        16.47        13.22         5.49         8.71 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 
       10.45        13.38        13.15        15.35        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.76        12.59        15.52        13.18        12.33        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       38.40        53.95        15.78         2.30        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        3.42        16.44        15.35         9.27         8.98        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I 
        1.55        18.31        28.11        46.19        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JE 
       18.21        25.08         2.10 

$`AMP PEAK 26(17Q12) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL 
        0.36         5.16        20.02        31.27         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 
        2.63        20.12        18.64         3.88         9.30         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH 
       21.70        24.03         6.28         3.16        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S 
       21.01        47.93         7.17         3.16         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK 
       25.12         3.75         3.02        55.50         2.66        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76        21.37        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 
       12.33        13.25        12.62        12.46        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 
       25.25        10.52        12.00        12.23        12.03        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6XQ 
        0.13        12.03        12.85        12.26        16.31         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-VR-A8EO TCGA-VR-A8EP 
        9.30         2.89         7.00         5.29        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       22.82         8.12        33.70        18.18        52.27        18.05 
TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                        0.30                         0.13 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                       60.39                       122.10 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                       13.22                        12.62 
[1] "0.3 - 60.4 (13.2)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1"  
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(17Q12) MUTATED         3        0        2        0        14
  AMP PEAK 26(17Q12) WILD-TYPE       5        5        4        1        33
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(17Q12) MUTATED          11        16          5          4
  AMP PEAK 26(17Q12) WILD-TYPE        20         9          9          5
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(17Q12) MUTATED            2        4         2
  AMP PEAK 26(17Q12) WILD-TYPE          5        1         2
D26V3, multiclass
            clus
vv           AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            0                            5
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          14                           33
  STAGE IIB                          11                           20
  STAGE III                          16                            9
  STAGE IIIA                          5                            9
  STAGE IIIB                          4                            5
  STAGE IIIC                          2                            5
  STAGE IV                            4                            1
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 26(17Q12) MUTATED      14 13 35  2
  AMP PEAK 26(17Q12) WILD-TYPE    18 30 52  3
D26V4, multiclass
       clus
vv      AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  T0+T1                         14                           18
  T2                            13                           30
  T3                            35                           52
  T4                             2                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 26(17Q12) MUTATED   23 33  5  3
  AMP PEAK 26(17Q12) WILD-TYPE 54 35  7  5
D26V5, multiclass
    clus
vv   AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  N0                         23                           54
  N1                         33                           35
  N2                          5                            7
  N3                          3                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED   50  6
  AMP PEAK 26(17Q12) WILD-TYPE 85  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED     50    6
  AMP PEAK 26(17Q12) WILD-TYPE   85    3
   clus
vv  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  0                         50                           85
  1                          6                            3
[1] 2 2
[1] FALSE
D26V7, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED    7 68
  AMP PEAK 26(17Q12) WILD-TYPE 20 89
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED      7   68
  AMP PEAK 26(17Q12) WILD-TYPE   20   89
        clus
vv       AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  FEMALE                          7                           20
  MALE                           68                           89
[1] 2 2
[1] FALSE
D26V8, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED   45 20
  AMP PEAK 26(17Q12) WILD-TYPE 78 23
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED     45   20
  AMP PEAK 26(17Q12) WILD-TYPE   78   23
     clus
vv    AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  NO                          45                           78
  YES                         20                           23
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED   46 29
  AMP PEAK 26(17Q12) WILD-TYPE 42 67
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED     46   29
  AMP PEAK 26(17Q12) WILD-TYPE   42   67
                                   clus
vv                                  AMP PEAK 26(17Q12) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             46
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         29
                                   clus
vv                                  AMP PEAK 26(17Q12) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               42
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           67
[1] 2 2
[1] FALSE
D26V11, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 26(17Q12) MUTATED   50  6  1  4
  AMP PEAK 26(17Q12) WILD-TYPE 87  6  1  3
D26V12, multiclass
    clus
vv   AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  R0                         50                           87
  R1                          6                            6
  R2                          1                            1
  RX                          4                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(17Q12) MUTATED      15                         3    47
  AMP PEAK 26(17Q12) WILD-TYPE    31                         2    67
D26V14, multiclass
                           clus
vv                          AMP PEAK 26(17Q12) MUTATED
  ASIAN                                             15
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             47
                           clus
vv                          AMP PEAK 26(17Q12) WILD-TYPE
  ASIAN                                               31
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED    2 34
  AMP PEAK 26(17Q12) WILD-TYPE  4 54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED      2   34
  AMP PEAK 26(17Q12) WILD-TYPE    4   54
                        clus
vv                       AMP PEAK 26(17Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         34
                        clus
vv                       AMP PEAK 26(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           54
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(18P11.32) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 27(18P11.32) MUTATED   43 26
  AMP PEAK 27(18P11.32) WILD-TYPE 65 50
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             69                             115 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             26                              50 
$`AMP PEAK 27(18P11.32) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-L5-A8NT 
       60.39        34.85         4.31         8.94         0.36        27.12 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A50L 
        7.63        13.94        16.24         4.21        32.45         0.53 
TCGA-IG-A625 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-L5-A43C 
       12.82        14.50        12.16        44.75         3.68         3.16 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       47.93         3.32         1.38         3.16         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
        2.60         2.66        13.48        16.47        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       21.37        46.09        10.36        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       15.35        12.59        13.25        12.62        12.46        12.76 
TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY 
       12.59        12.33        13.22         4.47        25.25        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6Y0 
       13.18        13.18        12.85        12.26         5.06        53.95 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EX TCGA-VR-A8EZ 
       12.69        20.38         3.42        16.44        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       52.27        11.24         9.17        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

$`AMP PEAK 27(18P11.32) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       58.55         5.92         8.94         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
        4.67       122.10        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        26.33        32.61        21.01        18.35         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        3.75         3.02        55.50        12.92        13.55         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A2 
       10.45        12.66        12.43        13.38        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HV 
       22.39        12.85        15.52        11.54        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.33        13.38         0.13        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        7.00         5.29        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       33.70        46.19        18.05        15.91        18.21        41.23 
TCGA-ZR-A9CJ 
       19.73 

  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                           0.36                            0.13 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                          60.39                          122.10 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                          12.62                           14.30 
[1] "0.4 - 60.4 (12.6)"  "0.1 - 122.1 (14.3)"
[1] "hr=" "1.1"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(18P11.32) MUTATED         1        2        3        0        17
  AMP PEAK 27(18P11.32) WILD-TYPE       7        3        3        1        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(18P11.32) MUTATED          10        13          5          1
  AMP PEAK 27(18P11.32) WILD-TYPE        21        12          9          8
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(18P11.32) MUTATED            4        3         3
  AMP PEAK 27(18P11.32) WILD-TYPE          3        2         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               2                               3
  STAGE IB                               3                               3
  STAGE II                               0                               1
  STAGE IIA                             17                              30
  STAGE IIB                             10                              21
  STAGE III                             13                              12
  STAGE IIIA                             5                               9
  STAGE IIIB                             1                               8
  STAGE IIIC                             4                               3
  STAGE IV                               3                               2
  STAGE IVA                              3                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 27(18P11.32) MUTATED       9 13 42  0
  AMP PEAK 27(18P11.32) WILD-TYPE    23 30 45  5
D27V4, multiclass
       clus
vv      AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  T0+T1                             9                              23
  T2                               13                              30
  T3                               42                              45
  T4                                0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 27(18P11.32) MUTATED   27 28  3  5
  AMP PEAK 27(18P11.32) WILD-TYPE 50 40  9  3
D27V5, multiclass
    clus
vv   AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  N0                            27                              50
  N1                            28                              40
  N2                             3                               9
  N3                             5                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED   49  6
  AMP PEAK 27(18P11.32) WILD-TYPE 86  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED     49    6
  AMP PEAK 27(18P11.32) WILD-TYPE   86    3
   clus
vv  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  0                            49                              86
  1                             6                               3
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED    5 64
  AMP PEAK 27(18P11.32) WILD-TYPE 22 93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED      5   64
  AMP PEAK 27(18P11.32) WILD-TYPE   22   93
        clus
vv       AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  FEMALE                             5                              22
  MALE                              64                              93
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED   44 18
  AMP PEAK 27(18P11.32) WILD-TYPE 79 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED     44   18
  AMP PEAK 27(18P11.32) WILD-TYPE   79   25
     clus
vv    AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  NO                             44                              79
  YES                            18                              25
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED   28 41
  AMP PEAK 27(18P11.32) WILD-TYPE 60 55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED     28   41
  AMP PEAK 27(18P11.32) WILD-TYPE   60   55
                                   clus
vv                                  AMP PEAK 27(18P11.32) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                28
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            41
                                   clus
vv                                  AMP PEAK 27(18P11.32) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  60
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              55
[1] 2 2
[1] FALSE
D27V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 27(18P11.32) MUTATED   55  4  1  3
  AMP PEAK 27(18P11.32) WILD-TYPE 82  8  1  4
D27V12, multiclass
    clus
vv   AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  R0                            55                              82
  R1                             4                               8
  R2                             1                               1
  RX                             3                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(18P11.32) MUTATED      23                         3    34
  AMP PEAK 27(18P11.32) WILD-TYPE    23                         2    80
D27V14, multiclass
                           clus
vv                          AMP PEAK 27(18P11.32) MUTATED
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                34
                           clus
vv                          AMP PEAK 27(18P11.32) WILD-TYPE
  ASIAN                                                  23
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED    3 32
  AMP PEAK 27(18P11.32) WILD-TYPE  3 56
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED      3   32
  AMP PEAK 27(18P11.32) WILD-TYPE    3   56
                        clus
vv                       AMP PEAK 27(18P11.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            32
                        clus
vv                       AMP PEAK 27(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              56
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(18Q11.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 28(18Q11.2) MUTATED   36 23
  AMP PEAK 28(18Q11.2) WILD-TYPE 72 53
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            59                            125 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            23                             53 
$`AMP PEAK 28(18Q11.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
       27.12        58.55         7.63        13.94         4.21        33.27 
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4ON 
        0.53        12.82        47.38         3.16        30.25        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE 
        3.32         3.16         7.13         2.60         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU 
        2.66        13.48        13.22         5.49        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 
       52.57        46.09        10.36         5.92        12.62        12.76 
TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FR 
       12.59        12.33        25.25        13.18        13.18        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.82         7.59         5.06        38.40        53.95        15.78 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.69        20.38        16.44        22.82        18.18        52.27 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       11.24        15.91         2.10         1.32         2.66 

$`AMP PEAK 28(18Q11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
        5.16        20.02        25.78        31.27        14.30         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NJ 
       15.48        25.12         7.40         3.75        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A56G TCGA-LN-A49L 
       13.55         7.76        21.37         8.71        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ 
       12.33        10.52        12.00        12.23        12.03        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-R6-A6DN 
       13.38         0.13        12.03        12.85        33.11         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       16.31         7.04         6.35         9.30         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00         5.29         3.42        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       28.11        33.70        46.19        18.05         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42        19.73 

  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                          0.36                           0.13 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                         83.24                         122.10 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                         12.82                          13.15 
[1] "0.4 - 83.2 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(18Q11.2) MUTATED         5        1        3        0         9
  AMP PEAK 28(18Q11.2) WILD-TYPE       3        4        3        1        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(18Q11.2) MUTATED           8        11          5          3
  AMP PEAK 28(18Q11.2) WILD-TYPE        23        14          9          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(18Q11.2) MUTATED            3        1         2
  AMP PEAK 28(18Q11.2) WILD-TYPE          4        4         2
D28V3, multiclass
            clus
vv           AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              4
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                             9                             38
  STAGE IIB                             8                             23
  STAGE III                            11                             14
  STAGE IIIA                            5                              9
  STAGE IIIB                            3                              6
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 28(18Q11.2) MUTATED      11 10 31  1
  AMP PEAK 28(18Q11.2) WILD-TYPE    21 33 56  4
D28V4, multiclass
       clus
vv      AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  T0+T1                           11                             21
  T2                              10                             33
  T3                              31                             56
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 28(18Q11.2) MUTATED   22 23  4  4
  AMP PEAK 28(18Q11.2) WILD-TYPE 55 45  8  4
D28V5, multiclass
    clus
vv   AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  N0                           22                             55
  N1                           23                             45
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED   41  3
  AMP PEAK 28(18Q11.2) WILD-TYPE 94  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED     41    3
  AMP PEAK 28(18Q11.2) WILD-TYPE   94    6
   clus
vv  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  0                           41                             94
  1                            3                              6
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(18Q11.2) MUTATED     8  51
  AMP PEAK 28(18Q11.2) WILD-TYPE  19 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED      8   51
  AMP PEAK 28(18Q11.2) WILD-TYPE   19  106
        clus
vv       AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  FEMALE                            8                             19
  MALE                             51                            106
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED   40 11
  AMP PEAK 28(18Q11.2) WILD-TYPE 83 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED     40   11
  AMP PEAK 28(18Q11.2) WILD-TYPE   83   32
     clus
vv    AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  NO                            40                             83
  YES                           11                             32
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED   39 20
  AMP PEAK 28(18Q11.2) WILD-TYPE 49 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED     39   20
  AMP PEAK 28(18Q11.2) WILD-TYPE   49   76
                                   clus
vv                                  AMP PEAK 28(18Q11.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               39
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           20
                                   clus
vv                                  AMP PEAK 28(18Q11.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 49
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             76
[1] 2 2
[1] FALSE
D28V11, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 28(18Q11.2) MUTATED   44  3  1  4
  AMP PEAK 28(18Q11.2) WILD-TYPE 93  9  1  3
D28V12, multiclass
    clus
vv   AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  R0                           44                             93
  R1                            3                              9
  R2                            1                              1
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(18Q11.2) MUTATED      11                         0    42
  AMP PEAK 28(18Q11.2) WILD-TYPE    35                         5    72
D28V14, multiclass
                           clus
vv                          AMP PEAK 28(18Q11.2) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               42
                           clus
vv                          AMP PEAK 28(18Q11.2) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED    1 24
  AMP PEAK 28(18Q11.2) WILD-TYPE  5 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED      1   24
  AMP PEAK 28(18Q11.2) WILD-TYPE    5   64
                        clus
vv                       AMP PEAK 28(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       AMP PEAK 28(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             64
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(19Q12) MUTATION ANALYSIS
D29V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 29(19Q12) MUTATED   32 23
  AMP PEAK 29(19Q12) WILD-TYPE 76 53
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          55                          129 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          23                           53 
$`AMP PEAK 29(19Q12) MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       24.00        35.97        27.12        31.27        58.55         7.63 
TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A97H 
        8.94         7.69        35.21         3.88        23.41        14.50 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
       47.38         3.16        26.33        32.61        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NK 
        1.38         3.16        58.59         3.75        55.50        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        5.49         8.71        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A4A4 TCGA-LN-A4A5 
        5.92        10.45        12.33        15.35        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ 
       12.85        12.00         0.13        12.85        12.26         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
       16.31        38.40        53.95        15.78        12.69        20.38 
TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       15.35        28.11        52.27        15.91        18.21        25.08 
TCGA-Z6-A8JE 
        2.10 

$`AMP PEAK 29(19Q12) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
       18.64         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       25.22        24.03         6.28        30.25         0.30        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       47.93         7.17         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       15.48         2.60        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.22         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       13.41        83.24        12.66        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.49        12.76        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       13.18        12.33        13.38        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.82         8.02         7.59         7.04         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
        1.55        18.31         8.12        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        11.24         9.17        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                        0.13                         0.30 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                       58.59                       122.10 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                       15.35                        12.76 
[1] "0.1 - 58.6 (15.3)"  "0.3 - 122.1 (12.8)"
[1] "hr=" "1.3"
D29V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(19Q12) MUTATED         2        1        2        1        12
  AMP PEAK 29(19Q12) WILD-TYPE       6        4        4        0        35
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(19Q12) MUTATED          12         7          3          2
  AMP PEAK 29(19Q12) WILD-TYPE        19        18         11          7
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 29(19Q12) MUTATED            2        0         2
  AMP PEAK 29(19Q12) WILD-TYPE          5        5         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            4
  STAGE IB                            2                            4
  STAGE II                            1                            0
  STAGE IIA                          12                           35
  STAGE IIB                          12                           19
  STAGE III                           7                           18
  STAGE IIIA                          3                           11
  STAGE IIIB                          2                            7
  STAGE IIIC                          2                            5
  STAGE IV                            0                            5
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 29(19Q12) MUTATED       9 14 24  1
  AMP PEAK 29(19Q12) WILD-TYPE    23 29 63  4
D29V4, multiclass
       clus
vv      AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  T0+T1                          9                           23
  T2                            14                           29
  T3                            24                           63
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 29(19Q12) MUTATED   20 22  3  2
  AMP PEAK 29(19Q12) WILD-TYPE 57 46  9  6
D29V5, multiclass
    clus
vv   AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  N0                         20                           57
  N1                         22                           46
  N2                          3                            9
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                              cls
clus                            0  1
  AMP PEAK 29(19Q12) MUTATED   37  2
  AMP PEAK 29(19Q12) WILD-TYPE 98  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED     37    2
  AMP PEAK 29(19Q12) WILD-TYPE   98    7
   clus
vv  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  0                         37                           98
  1                          2                            7
[1] 2 2
[1] FALSE
D29V7, binary
                              cls
clus                             0   1
  AMP PEAK 29(19Q12) MUTATED     4  51
  AMP PEAK 29(19Q12) WILD-TYPE  23 106
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED      4   51
  AMP PEAK 29(19Q12) WILD-TYPE   23  106
        clus
vv       AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  FEMALE                          4                           23
  MALE                           51                          106
[1] 2 2
[1] FALSE
D29V8, binary
                              cls
clus                            0  1
  AMP PEAK 29(19Q12) MUTATED   41  9
  AMP PEAK 29(19Q12) WILD-TYPE 82 34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED     41    9
  AMP PEAK 29(19Q12) WILD-TYPE   82   34
     clus
vv    AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  NO                          41                           82
  YES                          9                           34
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, binary
                              cls
clus                            0  1
  AMP PEAK 29(19Q12) MUTATED   32 23
  AMP PEAK 29(19Q12) WILD-TYPE 56 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED     32   23
  AMP PEAK 29(19Q12) WILD-TYPE   56   73
                                   clus
vv                                  AMP PEAK 29(19Q12) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             32
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         23
                                   clus
vv                                  AMP PEAK 29(19Q12) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               56
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           73
[1] 2 2
[1] FALSE
D29V11, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 29(19Q12) MUTATED   40  2  1  2
  AMP PEAK 29(19Q12) WILD-TYPE 97 10  1  5
D29V12, multiclass
    clus
vv   AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  R0                         40                           97
  R1                          2                           10
  R2                          1                            1
  RX                          2                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(19Q12) MUTATED      12                         3    34
  AMP PEAK 29(19Q12) WILD-TYPE    34                         2    80
D29V14, multiclass
                           clus
vv                          AMP PEAK 29(19Q12) MUTATED
  ASIAN                                             12
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             34
                           clus
vv                          AMP PEAK 29(19Q12) WILD-TYPE
  ASIAN                                               34
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                              cls
clus                            0  1
  AMP PEAK 29(19Q12) MUTATED    2 27
  AMP PEAK 29(19Q12) WILD-TYPE  4 61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED      2   27
  AMP PEAK 29(19Q12) WILD-TYPE    4   61
                        clus
vv                       AMP PEAK 29(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         27
                        clus
vv                       AMP PEAK 29(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           61
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(XQ28) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 30(XQ28) MUTATED   38 31
  AMP PEAK 30(XQ28) WILD-TYPE 70 45
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         69                         115 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         31                          45 
$`AMP PEAK 30(XQ28) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00        19.99        20.02 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
       14.30         5.92        16.24        35.21        20.78         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03        23.41        12.82         9.96         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON 
      122.10        44.75        23.18        30.25        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        1.38        13.55        21.37        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X 
       12.66        12.43        12.33        13.38        12.59        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        12.49        12.59        22.39        13.22        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        13.18        13.18         0.13        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RB 
        8.02        16.31        15.78         2.89        12.69         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       15.35         8.98        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 
       52.27        46.19        11.24        15.91        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        3.42         2.10        19.73 

$`AMP PEAK 30(XQ28) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         8.94         4.70        22.82         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ 
       35.97        27.12         5.16        25.78        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63        13.94         8.94         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27         0.85         2.63        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE 
        0.79        14.86        14.50        12.16        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49O TCGA-LN-A49S 
       83.24        52.57        46.09        10.85        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 
       15.35        13.25        12.46        12.76        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        12.33         4.47        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.03        12.33        13.38        12.03        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.30         7.00        20.38         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A9VB 
       28.11        18.05         9.17        18.21        41.23         1.32 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                       0.13                        0.30 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                     122.10                       83.24 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                      13.22                       12.76 
[1] "0.1 - 122.1 (13.2)" "0.3 - 83.2 (12.8)" 
[1] "hr=" "1.2"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(XQ28) MUTATED         2        1        0        0        20
  AMP PEAK 30(XQ28) WILD-TYPE       6        4        6        1        27
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(XQ28) MUTATED          14         5          7          6
  AMP PEAK 30(XQ28) WILD-TYPE        17        20          7          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 30(XQ28) MUTATED            4        2         2
  AMP PEAK 30(XQ28) WILD-TYPE          3        3         2
D30V3, multiclass
            clus
vv           AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           1                           4
  STAGE IB                           0                           6
  STAGE II                           0                           1
  STAGE IIA                         20                          27
  STAGE IIB                         14                          17
  STAGE III                          5                          20
  STAGE IIIA                         7                           7
  STAGE IIIB                         6                           3
  STAGE IIIC                         4                           3
  STAGE IV                           2                           3
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK 30(XQ28) MUTATED       9 17 36  2
  AMP PEAK 30(XQ28) WILD-TYPE    23 26 51  3
D30V4, multiclass
       clus
vv      AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  T0+T1                         9                          23
  T2                           17                          26
  T3                           36                          51
  T4                            2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK 30(XQ28) MUTATED   30 22  7  5
  AMP PEAK 30(XQ28) WILD-TYPE 47 46  5  3
D30V5, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  N0                        30                          47
  N1                        22                          46
  N2                         7                           5
  N3                         5                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                             cls
clus                           0  1
  AMP PEAK 30(XQ28) MUTATED   48  4
  AMP PEAK 30(XQ28) WILD-TYPE 87  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     48    4
  AMP PEAK 30(XQ28) WILD-TYPE   87    5
   clus
vv  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  0                        48                          87
  1                         4                           5
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                           0  1
  AMP PEAK 30(XQ28) MUTATED    6 63
  AMP PEAK 30(XQ28) WILD-TYPE 21 94
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      6   63
  AMP PEAK 30(XQ28) WILD-TYPE   21   94
        clus
vv       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  FEMALE                         6                          21
  MALE                          63                          94
[1] 2 2
[1] FALSE
D30V8, binary
                             cls
clus                           0  1
  AMP PEAK 30(XQ28) MUTATED   45 16
  AMP PEAK 30(XQ28) WILD-TYPE 78 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     45   16
  AMP PEAK 30(XQ28) WILD-TYPE   78   27
     clus
vv    AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  NO                         45                          78
  YES                        16                          27
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, binary
                             cls
clus                           0  1
  AMP PEAK 30(XQ28) MUTATED   24 45
  AMP PEAK 30(XQ28) WILD-TYPE 64 51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     24   45
  AMP PEAK 30(XQ28) WILD-TYPE   64   51
                                   clus
vv                                  AMP PEAK 30(XQ28) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                            24
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                        45
                                   clus
vv                                  AMP PEAK 30(XQ28) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                              64
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          51
[1] 2 2
[1] FALSE
D30V11, continuous
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK 30(XQ28) MUTATED   50  4  1  4
  AMP PEAK 30(XQ28) WILD-TYPE 87  8  1  3
D30V12, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  R0                        50                          87
  R1                         4                           8
  R2                         1                           1
  RX                         4                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(XQ28) MUTATED      26                         3    36
  AMP PEAK 30(XQ28) WILD-TYPE    20                         2    78
D30V14, multiclass
                           clus
vv                          AMP PEAK 30(XQ28) MUTATED
  ASIAN                                            26
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            36
                           clus
vv                          AMP PEAK 30(XQ28) WILD-TYPE
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                             cls
clus                           0  1
  AMP PEAK 30(XQ28) MUTATED    4 40
  AMP PEAK 30(XQ28) WILD-TYPE  2 48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      4   40
  AMP PEAK 30(XQ28) WILD-TYPE    2   48
                        clus
vv                       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             4                           2
  NOT HISPANIC OR LATINO                        40                          48
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   42 33
  DEL PEAK  1(1P36.11) WILD-TYPE 66 43
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            75                            109 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            33                             43 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       35.97        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FH 
       18.64         3.88         0.53        12.82       122.10        47.38 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       23.18         0.30        26.33         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A893 
       29.00         7.13         7.43         2.60         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
       55.50        12.92        16.47        13.22         5.49        13.41 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
        5.92        13.38        13.25        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        13.18        12.33        12.85         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        5.06         2.89         2.30        20.38         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-XP-A8T8 
        8.12        28.11        33.70        52.27        25.08        14.37 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        34.85        18.28        19.99        22.82        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 
        5.16        20.02        25.78         5.92         4.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.78         2.63        20.12         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       44.75        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH 
       25.22        24.03         6.28         3.16        30.25        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK 
       15.48        25.12         3.75         2.66        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.15        15.35        12.59        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.23        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.82        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30        15.78        12.69         7.00         5.29 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       15.35        25.81        18.31        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        15.91        18.21        41.23         3.42 
TCGA-Z6-A8JE 
        2.10 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         12.85                          13.18 
[1] "0.3 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         5        1        2        0        14
  DEL PEAK  1(1P36.11) WILD-TYPE       3        4        4        1        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          15        14          3          6
  DEL PEAK  1(1P36.11) WILD-TYPE        16        11         11          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED            1        2         2
  DEL PEAK  1(1P36.11) WILD-TYPE          6        3         2
D31V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            14                             33
  STAGE IIB                            15                             16
  STAGE III                            14                             11
  STAGE IIIA                            3                             11
  STAGE IIIB                            6                              3
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  1(1P36.11) MUTATED      16 15 35  1
  DEL PEAK  1(1P36.11) WILD-TYPE    16 28 52  4
D31V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                           16                             16
  T2                              15                             28
  T3                              35                             52
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK  1(1P36.11) MUTATED   25 34  7  1
  DEL PEAK  1(1P36.11) WILD-TYPE 52 34  5  7
D31V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           25                             52
  N1                           34                             34
  N2                            7                              5
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   54  4
  DEL PEAK  1(1P36.11) WILD-TYPE 81  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     54    4
  DEL PEAK  1(1P36.11) WILD-TYPE   81    5
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           54                             81
  1                            4                              5
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED    9 66
  DEL PEAK  1(1P36.11) WILD-TYPE 18 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      9   66
  DEL PEAK  1(1P36.11) WILD-TYPE   18   91
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                            9                             18
  MALE                             66                             91
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   53 12
  DEL PEAK  1(1P36.11) WILD-TYPE 70 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     53   12
  DEL PEAK  1(1P36.11) WILD-TYPE   70   31
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            53                             70
  YES                           12                             31
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   44 31
  DEL PEAK  1(1P36.11) WILD-TYPE 44 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     44   31
  DEL PEAK  1(1P36.11) WILD-TYPE   44   65
                                   clus
vv                                  DEL PEAK  1(1P36.11) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           31
                                   clus
vv                                  DEL PEAK  1(1P36.11) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             65
[1] 2 2
[1] FALSE
D31V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.11) MUTATED   56  6  0  3
  DEL PEAK  1(1P36.11) WILD-TYPE 81  6  2  4
D31V12, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           56                             81
  R1                            6                              6
  R2                            0                              2
  RX                            3                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED      14                         3    46
  DEL PEAK  1(1P36.11) WILD-TYPE    32                         2    68
D31V14, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               46
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                              2
  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"
D31V15, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED    2 29
  DEL PEAK  1(1P36.11) WILD-TYPE  4 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      2   29
  DEL PEAK  1(1P36.11) WILD-TYPE    4   59
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             59
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.2) MUTATED   38 26
  DEL PEAK  2(1P13.2) WILD-TYPE 70 50
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           64                           120 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           26                            50 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-2H-A9GI 
        8.94        24.00         4.70         0.36        35.97        14.30 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        7.63        13.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       35.21         2.63        18.64         3.88         0.53         0.79 
TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU 
        4.67         3.68         0.30        32.61         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE 
        7.13         7.43        15.48         2.60         7.40        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K 
        2.66        12.92        13.48        16.47        13.41         5.92 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       13.25        12.59        12.59        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.00        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
       12.85        12.26        33.11         7.59        53.95         2.89 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        2.30        20.38         3.42         9.27         8.98        12.43 
TCGA-VR-A8EW TCGA-VR-AA4D TCGA-XP-A8T8 TCGA-Z6-A9VB 
        8.12        46.19        14.37         1.32 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         4.31        19.99 
TCGA-L5-A88T TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82        27.12         5.16        20.02        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3Y9 TCGA-IG-A3YA 
       58.55         5.92         8.94        16.24         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ 
       24.03         6.28         3.16        30.25        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NL 
       58.59        25.12         3.75         3.02        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.62        12.46        12.49        12.76        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY 
       15.52        12.33        13.22         4.47        12.23        12.03 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        12.03         7.82         8.02         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        38.40         6.35         9.30        15.78        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00         5.29        16.44        15.35        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82         1.55        18.31        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23         3.42         2.10         2.66        19.73 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.30                          0.13 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         55.5                         122.1 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       12.295                        14.680 
[1] "0.3 - 55.5 (12.3)"  "0.1 - 122.1 (14.7)"
[1] "hr=" "1.4"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        0        3        0        17
  DEL PEAK  2(1P13.2) WILD-TYPE       6        5        3        1        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          11        12          3          4
  DEL PEAK  2(1P13.2) WILD-TYPE        20        13         11          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P13.2) MUTATED            0        2         1
  DEL PEAK  2(1P13.2) WILD-TYPE          7        3         3
D32V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             3                             3
  STAGE II                             0                             1
  STAGE IIA                           17                            30
  STAGE IIB                           11                            20
  STAGE III                           12                            13
  STAGE IIIA                           3                            11
  STAGE IIIB                           4                             5
  STAGE IIIC                           0                             7
  STAGE IV                             2                             3
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  2(1P13.2) MUTATED      10 16 30  1
  DEL PEAK  2(1P13.2) WILD-TYPE    22 27 57  4
D32V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                          10                            22
  T2                             16                            27
  T3                             30                            57
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  2(1P13.2) MUTATED   25 27  5  0
  DEL PEAK  2(1P13.2) WILD-TYPE 52 41  7  8
D32V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          25                            52
  N1                          27                            41
  N2                           5                             7
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   48  3
  DEL PEAK  2(1P13.2) WILD-TYPE 87  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     48    3
  DEL PEAK  2(1P13.2) WILD-TYPE   87    6
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          48                            87
  1                           3                             6
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     7  57
  DEL PEAK  2(1P13.2) WILD-TYPE  20 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7   57
  DEL PEAK  2(1P13.2) WILD-TYPE   20  100
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           7                            20
  MALE                            57                           100
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   42 15
  DEL PEAK  2(1P13.2) WILD-TYPE 81 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     42   15
  DEL PEAK  2(1P13.2) WILD-TYPE   81   28
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           42                            81
  YES                          15                            28
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   32 32
  DEL PEAK  2(1P13.2) WILD-TYPE 56 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     32   32
  DEL PEAK  2(1P13.2) WILD-TYPE   56   64
                                   clus
vv                                  DEL PEAK  2(1P13.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              32
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          32
                                   clus
vv                                  DEL PEAK  2(1P13.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                56
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            64
[1] 2 2
[1] FALSE
D32V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  2(1P13.2) MUTATED   47  5  0  2
  DEL PEAK  2(1P13.2) WILD-TYPE 90  7  2  5
D32V12, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          47                            90
  R1                           5                             7
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.2) MUTATED      18                         2    35
  DEL PEAK  2(1P13.2) WILD-TYPE    28                         3    79
D32V14, multiclass
                           clus
vv                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              35
                           clus
vv                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    1 32
  DEL PEAK  2(1P13.2) WILD-TYPE  5 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1   32
  DEL PEAK  2(1P13.2) WILD-TYPE    5   56
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            56
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED     8   9
  DEL PEAK  3(1Q44) WILD-TYPE 100  67
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         167 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          9                          67 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.00        35.97         3.88         9.96        21.01         3.32 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 
       83.24        10.36         5.92        13.41        12.46        22.39 
TCGA-LN-A7HW TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-VR-A8ER TCGA-VR-AA7D 
       12.00         7.59        53.95        12.43         9.17 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        52.57        46.09        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       3.32                        0.13 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      12.43                       13.18 
[1] "3.3 - 83.2 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D33V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         1        0        0        0         6
  DEL PEAK  3(1Q44) WILD-TYPE       7        5        6        1        41
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           1         2          0          2
  DEL PEAK  3(1Q44) WILD-TYPE        30        23         14          7
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(1Q44) MUTATED            3        0         0
  DEL PEAK  3(1Q44) WILD-TYPE          4        5         4
D33V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            1                           7
  STAGE IA                           0                           5
  STAGE IB                           0                           6
  STAGE II                           0                           1
  STAGE IIA                          6                          41
  STAGE IIB                          1                          30
  STAGE III                          2                          23
  STAGE IIIA                         0                          14
  STAGE IIIB                         2                           7
  STAGE IIIC                         3                           4
  STAGE IV                           0                           5
  STAGE IVA                          0                           4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK  3(1Q44) MUTATED       1  4  9  1
  DEL PEAK  3(1Q44) WILD-TYPE    31 39 78  4
D33V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         1                          31
  T2                            4                          39
  T3                            9                          78
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK  3(1Q44) MUTATED    7  3  2  3
  DEL PEAK  3(1Q44) WILD-TYPE 70 65 10  5
D33V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         7                          70
  N1                         3                          65
  N2                         2                          10
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    13   0
  DEL PEAK  3(1Q44) WILD-TYPE 122   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     13    0
  DEL PEAK  3(1Q44) WILD-TYPE  122    9
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        13                         122
  1                         0                           9
[1] 2 2
[1] FALSE
D33V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     2  15
  DEL PEAK  3(1Q44) WILD-TYPE  25 142
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      2   15
  DEL PEAK  3(1Q44) WILD-TYPE   25  142
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         2                          25
  MALE                          15                         142
[1] 2 2
[1] FALSE
D33V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    10   4
  DEL PEAK  3(1Q44) WILD-TYPE 113  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     10    4
  DEL PEAK  3(1Q44) WILD-TYPE  113   39
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                         10                         113
  YES                         4                          39
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    9  8
  DEL PEAK  3(1Q44) WILD-TYPE 79 88
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      9    8
  DEL PEAK  3(1Q44) WILD-TYPE   79   88
                                   clus
vv                                  DEL PEAK  3(1Q44) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             9
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         8
                                   clus
vv                                  DEL PEAK  3(1Q44) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                              79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          88
[1] 2 2
[1] FALSE
D33V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  3(1Q44) MUTATED    13   1   0   1
  DEL PEAK  3(1Q44) WILD-TYPE 124  11   2   6
D33V12, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  R0                        13                         124
  R1                         1                          11
  R2                         0                           2
  RX                         1                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED       5                         0    10
  DEL PEAK  3(1Q44) WILD-TYPE    41                         5   104
D33V14, multiclass
                           clus
vv                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            10
                           clus
vv                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              41
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    0 10
  DEL PEAK  3(1Q44) WILD-TYPE  6 78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   10
  DEL PEAK  3(1Q44) WILD-TYPE    6   78
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           6
  NOT HISPANIC OR LATINO                        10                          78
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q22.1) MUTATED   35 24
  DEL PEAK  4(2Q22.1) WILD-TYPE 73 52
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           59                           125 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           24                            52 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       24.00         5.16        58.55         4.21        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12        18.64         0.53        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        9.96         4.67        12.16        44.75        68.02        41.52 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A893 
        3.16         0.30        58.59         7.43         7.40         3.02 
TCGA-L5-A8NK TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
       13.55        52.57        10.36        10.45        12.46        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6XG TCGA-R6-A6Y0 
       12.33        13.18         0.13        12.85        38.40        53.95 
TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        2.89        20.38         5.29        12.43        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       33.70        18.18        52.27        11.24        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         1.32         2.66 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       20.02        25.78        31.27        14.30         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       13.94         8.94        16.24        32.45         7.69        35.21 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
       20.78         3.88         9.30        23.41        12.82        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       14.50       122.10         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF 
       31.56        25.22        24.03         6.28        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60        25.12         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        8.71        13.41        83.24        46.09        10.85         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR 
       13.22        25.25        12.03        13.38        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04         6.35         9.30        15.78         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4D 
       25.81        27.09        22.82         1.55        28.11        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.05         9.17        18.21         2.10        19.73 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.13                          0.36 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        12.33                         13.38 
[1] "0.1 - 68.0 (12.3)"  "0.4 - 122.1 (13.4)"
[1] "hr=" "1"  
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         2        0        2        0        19
  DEL PEAK  4(2Q22.1) WILD-TYPE       6        5        4        1        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED          10         6          6          4
  DEL PEAK  4(2Q22.1) WILD-TYPE        21        19          8          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q22.1) MUTATED            2        3         0
  DEL PEAK  4(2Q22.1) WILD-TYPE          5        2         4
D34V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           19                            28
  STAGE IIB                           10                            21
  STAGE III                            6                            19
  STAGE IIIA                           6                             8
  STAGE IIIB                           4                             5
  STAGE IIIC                           2                             5
  STAGE IV                             3                             2
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  4(2Q22.1) MUTATED       7 18 27  3
  DEL PEAK  4(2Q22.1) WILD-TYPE    25 25 60  2
D34V4, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T0+T1                           7                            25
  T2                             18                            25
  T3                             27                            60
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  4(2Q22.1) MUTATED   25 23  4  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 52 45  8  5
D34V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          25                            52
  N1                          23                            45
  N2                           4                             8
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED   48  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 87  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     48    3
  DEL PEAK  4(2Q22.1) WILD-TYPE   87    6
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                          48                            87
  1                           3                             6
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    11  48
  DEL PEAK  4(2Q22.1) WILD-TYPE  16 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     11   48
  DEL PEAK  4(2Q22.1) WILD-TYPE   16  109
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                          11                            16
  MALE                            48                           109
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED   43 13
  DEL PEAK  4(2Q22.1) WILD-TYPE 80 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     43   13
  DEL PEAK  4(2Q22.1) WILD-TYPE   80   30
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                           43                            80
  YES                          13                            30
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED   13 46
  DEL PEAK  4(2Q22.1) WILD-TYPE 75 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     13   46
  DEL PEAK  4(2Q22.1) WILD-TYPE   75   50
                                   clus
vv                                  DEL PEAK  4(2Q22.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              13
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          46
                                   clus
vv                                  DEL PEAK  4(2Q22.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            50
[1] 2 2
[1] FALSE
D34V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  4(2Q22.1) MUTATED   46  4  2  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 91  8  0  4
D34V12, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                          46                            91
  R1                           4                             8
  R2                           2                             0
  RX                           3                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED      18                         2    35
  DEL PEAK  4(2Q22.1) WILD-TYPE    28                         3    79
D34V14, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              35
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    4 33
  DEL PEAK  4(2Q22.1) WILD-TYPE  2 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      4   33
  DEL PEAK  4(2Q22.1) WILD-TYPE    2   55
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          33
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            55
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q33.3) MUTATED   26 10
  DEL PEAK  5(2Q33.3) WILD-TYPE 82 66
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           36                           148 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           10                            66 
$`DEL PEAK  5(2Q33.3) MUTATED`
TCGA-S8-A6BV TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.02        35.21         0.85         2.63        20.12        18.64 
TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A88S 
        0.79        68.02        25.22         0.30        58.59        15.48 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49V 
        3.02        16.47        13.55         5.49         5.92        12.59 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.33        10.52        12.23        13.18        12.33        13.38 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26         8.02         2.89         2.30        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       12.43        52.27        25.08         1.32         2.66        19.73 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.12         5.16        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT 
       32.45         7.69        33.27        20.78         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I1 
        4.47        12.33        25.25        12.00        12.03        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.13        12.03        12.85        33.11         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        3.42        16.44        15.35         9.27         8.98        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       41.23        14.37         3.42         2.10 

  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                         0.30                          0.13 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                       12.510                        13.165 
[1] "0.3 - 68.0 (12.5)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q33.3) MUTATED         1        0        2        0        12
  DEL PEAK  5(2Q33.3) WILD-TYPE       7        5        4        1        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q33.3) MUTATED           4         5          7          1
  DEL PEAK  5(2Q33.3) WILD-TYPE        27        20          7          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(2Q33.3) MUTATED            1        0         0
  DEL PEAK  5(2Q33.3) WILD-TYPE          6        5         4
D35V3, multiclass
            clus
vv           DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             5
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           12                            35
  STAGE IIB                            4                            27
  STAGE III                            5                            20
  STAGE IIIA                           7                             7
  STAGE IIIB                           1                             8
  STAGE IIIC                           1                             6
  STAGE IV                             0                             5
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  5(2Q33.3) MUTATED       1 10 20  2
  DEL PEAK  5(2Q33.3) WILD-TYPE    31 33 67  3
D35V4, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T0+T1                           1                            31
  T2                             10                            33
  T3                             20                            67
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  5(2Q33.3) MUTATED   16 15  1  1
  DEL PEAK  5(2Q33.3) WILD-TYPE 61 53 11  7
D35V5, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                          16                            61
  N1                          15                            53
  N2                           1                            11
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED    30   0
  DEL PEAK  5(2Q33.3) WILD-TYPE 105   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     30    0
  DEL PEAK  5(2Q33.3) WILD-TYPE  105    9
   clus
vv  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  0                          30                           105
  1                           0                             9
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED     4  32
  DEL PEAK  5(2Q33.3) WILD-TYPE  23 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      4   32
  DEL PEAK  5(2Q33.3) WILD-TYPE   23  125
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                           4                            23
  MALE                            32                           125
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED   24  9
  DEL PEAK  5(2Q33.3) WILD-TYPE 99 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     24    9
  DEL PEAK  5(2Q33.3) WILD-TYPE   99   34
     clus
vv    DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  NO                           24                            99
  YES                           9                            34
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED   10 26
  DEL PEAK  5(2Q33.3) WILD-TYPE 78 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     10   26
  DEL PEAK  5(2Q33.3) WILD-TYPE   78   70
                                   clus
vv                                  DEL PEAK  5(2Q33.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              10
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          26
                                   clus
vv                                  DEL PEAK  5(2Q33.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            70
[1] 2 2
[1] FALSE
D35V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q33.3) MUTATED    30   3   0   0
  DEL PEAK  5(2Q33.3) WILD-TYPE 107   9   2   7
D35V12, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  R0                          30                           107
  R1                           3                             9
  R2                           0                             2
  RX                           0                             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"
D35V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q33.3) MUTATED      10                         1    24
  DEL PEAK  5(2Q33.3) WILD-TYPE    36                         4    90
D35V14, multiclass
                           clus
vv                          DEL PEAK  5(2Q33.3) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              24
                           clus
vv                          DEL PEAK  5(2Q33.3) WILD-TYPE
  ASIAN                                                36
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED    1 22
  DEL PEAK  5(2Q33.3) WILD-TYPE  5 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      1   22
  DEL PEAK  5(2Q33.3) WILD-TYPE    5   66
                        clus
vv                       DEL PEAK  5(2Q33.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          22
                        clus
vv                       DEL PEAK  5(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            66
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  6(3P26.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P26.2) MUTATED   74 37
  DEL PEAK  6(3P26.2) WILD-TYPE 34 39
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          111                            73 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           37                            39 
$`DEL PEAK  6(3P26.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A8NG TCGA-S8-A6BV 
       60.39         4.31         8.94         4.70        35.97        20.02 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12         3.88         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H 
        9.96        14.50        12.16        68.02        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        47.93         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE 
        4.90         7.13        15.48         2.60         7.40        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV 
        2.66        12.92        16.47        13.55         5.49        52.57 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85         5.92        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.85        12.26        33.11         7.82         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
       38.40         2.89        12.69         7.00        20.38         3.42 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        3.42         2.10         1.32 

$`DEL PEAK  6(3P26.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28        24.00        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ 
        0.36        27.12         5.16        25.78        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP 
        7.63        32.45        18.64         9.30        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        3.16        26.33        21.01        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL 
        7.43        25.12         3.75         3.02        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        7.76        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       10.36        10.45        12.66        12.59        13.25        12.59 
TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       11.54        12.03         8.02         5.06        16.31         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30        15.78         2.30         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-Z6-AAPN 
       15.35         8.98        22.82         1.55        28.11         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                         0.13                          0.36 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                        12.62                         15.35 
[1] "0.1 - 68.0 (12.6)"  "0.4 - 122.1 (15.3)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P26.2) MUTATED         4        3        3        1        34
  DEL PEAK  6(3P26.2) WILD-TYPE       4        2        3        0        13
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.2) MUTATED          17        15         10          4
  DEL PEAK  6(3P26.2) WILD-TYPE        14        10          4          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(3P26.2) MUTATED            3        5         2
  DEL PEAK  6(3P26.2) WILD-TYPE          4        0         2
D36V3, multiclass
            clus
vv           DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             3                             2
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           34                            13
  STAGE IIB                           17                            14
  STAGE III                           15                            10
  STAGE IIIA                          10                             4
  STAGE IIIB                           4                             5
  STAGE IIIC                           3                             4
  STAGE IV                             5                             0
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  6(3P26.2) MUTATED      18 27 54  4
  DEL PEAK  6(3P26.2) WILD-TYPE    14 16 33  1
D36V4, multiclass
       clus
vv      DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  T0+T1                          18                            14
  T2                             27                            16
  T3                             54                            33
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  6(3P26.2) MUTATED   51 41  6  4
  DEL PEAK  6(3P26.2) WILD-TYPE 26 27  6  4
D36V5, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  N0                          51                            26
  N1                          41                            27
  N2                           6                             6
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   86  7
  DEL PEAK  6(3P26.2) WILD-TYPE 49  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     86    7
  DEL PEAK  6(3P26.2) WILD-TYPE   49    2
   clus
vv  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  0                          86                            49
  1                           7                             2
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   19 92
  DEL PEAK  6(3P26.2) WILD-TYPE  8 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     19   92
  DEL PEAK  6(3P26.2) WILD-TYPE    8   65
        clus
vv       DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  FEMALE                          19                             8
  MALE                            92                            65
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   76 27
  DEL PEAK  6(3P26.2) WILD-TYPE 47 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     76   27
  DEL PEAK  6(3P26.2) WILD-TYPE   47   16
     clus
vv    DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  NO                           76                            47
  YES                          27                            16
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   39 72
  DEL PEAK  6(3P26.2) WILD-TYPE 49 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     39   72
  DEL PEAK  6(3P26.2) WILD-TYPE   49   24
                                   clus
vv                                  DEL PEAK  6(3P26.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              39
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          72
                                   clus
vv                                  DEL PEAK  6(3P26.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                49
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            24
[1] 2 2
[1] FALSE
D36V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  6(3P26.2) MUTATED   85  7  2  5
  DEL PEAK  6(3P26.2) WILD-TYPE 52  5  0  2
D36V12, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  R0                          85                            52
  R1                           7                             5
  R2                           2                             0
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.2) MUTATED      35                         4    61
  DEL PEAK  6(3P26.2) WILD-TYPE    11                         1    53
D36V14, multiclass
                           clus
vv                          DEL PEAK  6(3P26.2) MUTATED
  ASIAN                                              35
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              61
                           clus
vv                          DEL PEAK  6(3P26.2) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED    4 61
  DEL PEAK  6(3P26.2) WILD-TYPE  2 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED      4   61
  DEL PEAK  6(3P26.2) WILD-TYPE    2   27
                        clus
vv                       DEL PEAK  6(3P26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK  6(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  7(3P14.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(3P14.3) MUTATED   80 46
  DEL PEAK  7(3P14.3) WILD-TYPE 28 30
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          126                            58 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           46                            30 
$`DEL PEAK  7(3P14.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31         8.94         4.70         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
        5.16        20.02        14.30         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        0.53        17.03         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       12.16        44.75        68.02        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93         3.32         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NF 
        7.13         7.43        15.48         2.60         7.40         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       12.92        16.47        13.55         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.03        12.85        12.26        33.11         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
       38.40         2.89        12.69         7.00        20.38         3.42 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

$`DEL PEAK  7(3P14.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28        24.00        19.99        22.82 
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A4QT 
       27.12        25.78        31.27        58.55         7.63         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       12.82        14.86         4.67       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        6.28         3.16        18.35         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI 
       29.00        25.12         3.75         3.02        55.50        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49V 
       13.22         7.76        21.37        46.09        10.36        12.59 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       11.54         7.82         8.02         5.06        16.31         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30        15.78         2.30         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
       15.35         8.98        22.82         1.55 

  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                         0.13                          1.55 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                       12.675                        15.730 
[1] "0.1 - 83.2 (12.7)"  "1.6 - 122.1 (15.7)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P14.3) MUTATED         5        2        3        1        40
  DEL PEAK  7(3P14.3) WILD-TYPE       3        3        3        0         7
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.3) MUTATED          20        18         11          4
  DEL PEAK  7(3P14.3) WILD-TYPE        11         7          3          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(3P14.3) MUTATED            4        4         3
  DEL PEAK  7(3P14.3) WILD-TYPE          3        1         1
D37V3, multiclass
            clus
vv           DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           40                             7
  STAGE IIB                           20                            11
  STAGE III                           18                             7
  STAGE IIIA                          11                             3
  STAGE IIIB                           4                             5
  STAGE IIIC                           4                             3
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  7(3P14.3) MUTATED      21 32 61  4
  DEL PEAK  7(3P14.3) WILD-TYPE    11 11 26  1
D37V4, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  T0+T1                          21                            11
  T2                             32                            11
  T3                             61                            26
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  7(3P14.3) MUTATED   59 46  7  5
  DEL PEAK  7(3P14.3) WILD-TYPE 18 22  5  3
D37V5, multiclass
    clus
vv   DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  N0                          59                            18
  N1                          46                            22
  N2                           7                             5
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   98  7
  DEL PEAK  7(3P14.3) WILD-TYPE 37  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     98    7
  DEL PEAK  7(3P14.3) WILD-TYPE   37    2
   clus
vv  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  0                          98                            37
  1                           7                             2
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.3) MUTATED    21 105
  DEL PEAK  7(3P14.3) WILD-TYPE   6  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     21  105
  DEL PEAK  7(3P14.3) WILD-TYPE    6   52
        clus
vv       DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  FEMALE                          21                             6
  MALE                           105                            52
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   84 32
  DEL PEAK  7(3P14.3) WILD-TYPE 39 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     84   32
  DEL PEAK  7(3P14.3) WILD-TYPE   39   11
     clus
vv    DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  NO                           84                            39
  YES                          32                            11
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   44 82
  DEL PEAK  7(3P14.3) WILD-TYPE 44 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     44   82
  DEL PEAK  7(3P14.3) WILD-TYPE   44   14
                                   clus
vv                                  DEL PEAK  7(3P14.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          82
                                   clus
vv                                  DEL PEAK  7(3P14.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            14
[1] 2 2
[1] FALSE
D37V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  7(3P14.3) MUTATED   97  7  2  5
  DEL PEAK  7(3P14.3) WILD-TYPE 40  5  0  2
D37V12, multiclass
    clus
vv   DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  R0                          97                            40
  R1                           7                             5
  R2                           2                             0
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.3) MUTATED      41                         4    67
  DEL PEAK  7(3P14.3) WILD-TYPE     5                         1    47
D37V14, multiclass
                           clus
vv                          DEL PEAK  7(3P14.3) MUTATED
  ASIAN                                              41
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              67
                           clus
vv                          DEL PEAK  7(3P14.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED    4 68
  DEL PEAK  7(3P14.3) WILD-TYPE  2 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED      4   68
  DEL PEAK  7(3P14.3) WILD-TYPE    2   20
                        clus
vv                       DEL PEAK  7(3P14.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK  7(3P14.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            20
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(3P14.2) MUTATED   78 47
  DEL PEAK  8(3P14.2) WILD-TYPE 30 29
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          125                            59 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           47                            29 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM 
       35.97         5.16        20.02        14.30         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H 
       14.50        12.16        44.75        68.02        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
        1.38         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        12.92        16.47        13.55         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.41        52.57        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        12.33        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.85        12.26        33.11         8.02         7.59         7.04 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89        12.69         7.00        20.38         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         3.42         2.10         1.32         2.66 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        60.39        34.85        19.99        22.82        27.12 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A4QT TCGA-IG-A625 
       25.78        31.27        58.55         7.63         9.30        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.86         4.67       122.10         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.16        18.35         3.16        58.59         4.90        29.00 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL 
       25.12         3.75         3.02        55.50        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49R 
        7.76        21.37        83.24        46.09        10.36        13.38 
TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.59        11.54         7.82         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB 
        6.35        53.95         9.30        15.78         2.30         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-ZR-A9CJ 
       15.35         8.98        22.82         1.55        19.73 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.13                          1.55 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        12.62                         15.78 
[1] "0.1 - 68.0 (12.6)"  "1.6 - 122.1 (15.8)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P14.2) MUTATED         4        2        4        1        39
  DEL PEAK  8(3P14.2) WILD-TYPE       4        3        2        0         8
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED          20        17         12          5
  DEL PEAK  8(3P14.2) WILD-TYPE        11         8          2          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(3P14.2) MUTATED            3        4         3
  DEL PEAK  8(3P14.2) WILD-TYPE          4        1         1
D38V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           39                             8
  STAGE IIB                           20                            11
  STAGE III                           17                             8
  STAGE IIIA                          12                             2
  STAGE IIIB                           5                             4
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  8(3P14.2) MUTATED      21 31 61  4
  DEL PEAK  8(3P14.2) WILD-TYPE    11 12 26  1
D38V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                          21                            11
  T2                             31                            12
  T3                             61                            26
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  8(3P14.2) MUTATED   58 46  8  4
  DEL PEAK  8(3P14.2) WILD-TYPE 19 22  4  4
D38V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          58                            19
  N1                          46                            22
  N2                           8                             4
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   96  7
  DEL PEAK  8(3P14.2) WILD-TYPE 39  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     96    7
  DEL PEAK  8(3P14.2) WILD-TYPE   39    2
   clus
vv  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  0                          96                            39
  1                           7                             2
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    21 104
  DEL PEAK  8(3P14.2) WILD-TYPE   6  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     21  104
  DEL PEAK  8(3P14.2) WILD-TYPE    6   53
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          21                             6
  MALE                           104                            53
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   82 33
  DEL PEAK  8(3P14.2) WILD-TYPE 41 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     82   33
  DEL PEAK  8(3P14.2) WILD-TYPE   41   10
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                           82                            41
  YES                          33                            10
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   44 81
  DEL PEAK  8(3P14.2) WILD-TYPE 44 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     44   81
  DEL PEAK  8(3P14.2) WILD-TYPE   44   15
                                   clus
vv                                  DEL PEAK  8(3P14.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          81
                                   clus
vv                                  DEL PEAK  8(3P14.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                44
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            15
[1] 2 2
[1] FALSE
D38V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(3P14.2) MUTATED   94  8  2  6
  DEL PEAK  8(3P14.2) WILD-TYPE 43  4  0  1
D38V12, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                          94                            43
  R1                           8                             4
  R2                           2                             0
  RX                           6                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED      40                         4    67
  DEL PEAK  8(3P14.2) WILD-TYPE     6                         1    47
D38V14, multiclass
                           clus
vv                          DEL PEAK  8(3P14.2) MUTATED
  ASIAN                                              40
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              67
                           clus
vv                          DEL PEAK  8(3P14.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED    4 67
  DEL PEAK  8(3P14.2) WILD-TYPE  2 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      4   67
  DEL PEAK  8(3P14.2) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK  8(3P14.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK  8(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            21
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  9(3Q11.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(3Q11.1) MUTATED   20 13
  DEL PEAK  9(3Q11.1) WILD-TYPE 88 63
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           33                           151 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           13                            63 
$`DEL PEAK  9(3Q11.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A88Y TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR 
       34.85         0.36        14.30        13.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A5S3 TCGA-JY-A6FD TCGA-L5-A43E 
        7.69         2.63        20.12        23.41        68.02        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A8NH TCGA-LN-A49L 
        0.30        32.61         3.32         7.43        12.92        10.45 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
       13.38        12.46        12.85         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       12.03        13.18        13.38         2.89        12.69         7.00 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR 
        9.27        46.19        18.21 

$`DEL PEAK  9(3Q11.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.02        25.78        31.27        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        16.24        33.27        35.21         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.00        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.30        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                         0.30                          0.13 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        12.69                         13.22 
[1] "0.3 - 68.0 (12.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3Q11.1) MUTATED         2        0        0        1         7
  DEL PEAK  9(3Q11.1) WILD-TYPE       6        5        6        0        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q11.1) MUTATED           8         5          2          0
  DEL PEAK  9(3Q11.1) WILD-TYPE        23        20         12          9
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(3Q11.1) MUTATED            1        2         0
  DEL PEAK  9(3Q11.1) WILD-TYPE          6        3         4
D39V3, multiclass
            clus
vv           DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             0                             6
  STAGE II                             1                             0
  STAGE IIA                            7                            40
  STAGE IIB                            8                            23
  STAGE III                            5                            20
  STAGE IIIA                           2                            12
  STAGE IIIB                           0                             9
  STAGE IIIC                           1                             6
  STAGE IV                             2                             3
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  9(3Q11.1) MUTATED       9  7 14  0
  DEL PEAK  9(3Q11.1) WILD-TYPE    23 36 73  5
D39V4, multiclass
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  T0+T1                           9                            23
  T2                              7                            36
  T3                             14                            73
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  9(3Q11.1) MUTATED   14 15  0  1
  DEL PEAK  9(3Q11.1) WILD-TYPE 63 53 12  7
D39V5, multiclass
    clus
vv   DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  N0                          14                            63
  N1                          15                            53
  N2                           0                            12
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED    26   2
  DEL PEAK  9(3Q11.1) WILD-TYPE 109   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED     26    2
  DEL PEAK  9(3Q11.1) WILD-TYPE  109    7
   clus
vv  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  0                          26                           109
  1                           2                             7
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED     3  30
  DEL PEAK  9(3Q11.1) WILD-TYPE  24 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      3   30
  DEL PEAK  9(3Q11.1) WILD-TYPE   24  127
        clus
vv       DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  FEMALE                           3                            24
  MALE                            30                           127
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED    23   7
  DEL PEAK  9(3Q11.1) WILD-TYPE 100  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED     23    7
  DEL PEAK  9(3Q11.1) WILD-TYPE  100   36
     clus
vv    DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  NO                           23                           100
  YES                           7                            36
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, binary
                               cls
clus                             0  1
  DEL PEAK  9(3Q11.1) MUTATED   18 15
  DEL PEAK  9(3Q11.1) WILD-TYPE 70 81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED     18   15
  DEL PEAK  9(3Q11.1) WILD-TYPE   70   81
                                   clus
vv                                  DEL PEAK  9(3Q11.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              18
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          15
                                   clus
vv                                  DEL PEAK  9(3Q11.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                70
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            81
[1] 2 2
[1] FALSE
D39V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3Q11.1) MUTATED    24   2   1   0
  DEL PEAK  9(3Q11.1) WILD-TYPE 113  10   1   7
D39V12, multiclass
    clus
vv   DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  R0                          24                           113
  R1                           2                            10
  R2                           1                             1
  RX                           0                             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"
D39V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q11.1) MUTATED      11                         0    18
  DEL PEAK  9(3Q11.1) WILD-TYPE    35                         5    96
D39V14, multiclass
                           clus
vv                          DEL PEAK  9(3Q11.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK  9(3Q11.1) WILD-TYPE
  ASIAN                                                35
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                               cls
clus                             0  1
  DEL PEAK  9(3Q11.1) MUTATED    1 18
  DEL PEAK  9(3Q11.1) WILD-TYPE  5 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      1   18
  DEL PEAK  9(3Q11.1) WILD-TYPE    5   70
                        clus
vv                       DEL PEAK  9(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       DEL PEAK  9(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            70
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(3Q26.31) MUTATED     5  11
  DEL PEAK 10(3Q26.31) WILD-TYPE 103  65
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            16                            168 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            11                             65 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IC-A6RE 
       34.85        18.28        25.78        14.30        13.94         7.69 
TCGA-JY-A93D TCGA-L5-A4OH TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NW 
       31.56        32.61         7.43         3.75        12.92        46.09 
TCGA-R6-A6DN TCGA-RE-A7BO TCGA-VR-A8EU TCGA-X8-AAAR 
        8.02         7.00        18.31        18.21 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       20.02        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          3.75                           0.13 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         46.09                         122.10 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                        16.255                         12.835 
[1] "3.8 - 46.1 (16.3)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.6"
D40V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         1        0        1        0         0
  DEL PEAK 10(3Q26.31) WILD-TYPE       7        5        5        1        47
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           5         2          1          0
  DEL PEAK 10(3Q26.31) WILD-TYPE        26        23         13          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(3Q26.31) MUTATED            1        2         0
  DEL PEAK 10(3Q26.31) WILD-TYPE          6        3         4
D40V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              5
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             0                             47
  STAGE IIB                             5                             26
  STAGE III                             2                             23
  STAGE IIIA                            1                             13
  STAGE IIIB                            0                              9
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 10(3Q26.31) MUTATED       7  3  5  0
  DEL PEAK 10(3Q26.31) WILD-TYPE    25 40 82  5
D40V4, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T0+T1                            7                             25
  T2                               3                             40
  T3                               5                             82
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 10(3Q26.31) MUTATED    3 11  0  1
  DEL PEAK 10(3Q26.31) WILD-TYPE 74 57 12  7
D40V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                            3                             74
  N1                           11                             57
  N2                            0                             12
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    11   2
  DEL PEAK 10(3Q26.31) WILD-TYPE 124   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     11    2
  DEL PEAK 10(3Q26.31) WILD-TYPE  124    7
   clus
vv  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  0                           11                            124
  1                            2                              7
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     1  15
  DEL PEAK 10(3Q26.31) WILD-TYPE  26 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1   15
  DEL PEAK 10(3Q26.31) WILD-TYPE   26  142
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                            1                             26
  MALE                             15                            142
[1] 2 2
[1] FALSE
D40V8, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    10   3
  DEL PEAK 10(3Q26.31) WILD-TYPE 113  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     10    3
  DEL PEAK 10(3Q26.31) WILD-TYPE  113   40
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  NO                            10                            113
  YES                            3                             40
[1] 2 2
[1] FALSE
D40V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 10(3Q26.31) MUTATED"
clus
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             1                             67 
                    TCGA-IG-A3I8                     TCGA-IG-A3QL 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A3YB                     TCGA-IG-A3YC 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A51D                     TCGA-IG-A5S3 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A7DP                     TCGA-KH-A6WC 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49K                     TCGA-LN-A49L 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49M                     TCGA-LN-A49N 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49O                     TCGA-LN-A49P 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49R                     TCGA-LN-A49S 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49U                     TCGA-LN-A49V 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49W                     TCGA-LN-A49X 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49Y                     TCGA-LN-A4A1 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A3 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A4                     TCGA-LN-A4A5 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A6                     TCGA-LN-A4A8 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A9                     TCGA-LN-A4MQ 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4MR                     TCGA-LN-A5U5 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A5U6                     TCGA-LN-A5U7 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HV                     TCGA-LN-A7HW 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HX                     TCGA-LN-A7HY 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HZ                     TCGA-V5-A7RB 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-V5-A7RC                     TCGA-V5-A7RE 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-V5-AASV                     TCGA-V5-AASW 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-V5-AASX                     TCGA-VR-A8EO 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EP                     TCGA-VR-A8EQ 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8ER                     TCGA-VR-A8ET 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EW                     TCGA-VR-A8EX 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EY                     TCGA-VR-A8EZ 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8Q7                     TCGA-VR-AA4D 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-AA4G                     TCGA-VR-AA7B 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-VR-AA7D                     TCGA-VR-AA7I 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-XP-A8T6                     TCGA-XP-A8T7 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-XP-A8T8                     TCGA-Z6-A8JD 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-Z6-A8JE 
"DEL PEAK 10(3Q26.31) WILD-TYPE" 
D40V10, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED   15  1
  DEL PEAK 10(3Q26.31) WILD-TYPE 73 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     15    1
  DEL PEAK 10(3Q26.31) WILD-TYPE   73   95
                                   clus
vv                                  DEL PEAK 10(3Q26.31) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               15
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            1
                                   clus
vv                                  DEL PEAK 10(3Q26.31) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             95
[1] 2 2
[1] FALSE
D40V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 10(3Q26.31) MUTATED    12   2   0   0
  DEL PEAK 10(3Q26.31) WILD-TYPE 125  10   2   7
D40V12, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  R0                           12                            125
  R1                            2                             10
  R2                            0                              2
  RX                            0                              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"
D40V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q26.31) MUTATED       0                         0    13
  DEL PEAK 10(3Q26.31) WILD-TYPE    46                         5   101
D40V14, multiclass
                           clus
vv                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               13
                           clus
vv                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                 46
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED    0  4
  DEL PEAK 10(3Q26.31) WILD-TYPE  6 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      0    4
  DEL PEAK 10(3Q26.31) WILD-TYPE    6   84
                        clus
vv                       DEL PEAK 10(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 10(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             84
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(4P15.2) MUTATED   60 46
  DEL PEAK 11(4P15.2) WILD-TYPE 48 30
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          106                            78 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           46                            30 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         8.94        24.00         4.70        35.97        27.12 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH 
       12.82         9.96         4.67        12.16        44.75        47.38 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
       25.22         3.16        21.01        47.93         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH 
        4.90         7.13         7.43         7.40         3.75        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         5.49         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43        13.38        15.35        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        12.76        12.85        15.52        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       25.25        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18         0.13        12.85        12.26         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06         7.04         6.35         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.38         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7I TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        14.37         3.42         1.32 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE 
        0.36         5.16        20.02        31.27         7.63         7.69 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H 
        2.63         9.30        17.03        23.41        14.86        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
      122.10        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        24.03         6.28        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       32.61        18.35         7.17         1.38        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         2.60        25.12         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49O 
       13.48         7.76        21.37        83.24        10.85        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.33        13.15        12.59        13.25        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FP 
       11.54        12.33         4.47        10.52        12.03        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
       33.11         7.82        16.31        38.40        53.95        15.78 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA7D 
        5.29        15.35        25.81        28.11        33.70         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        25.08        41.23         2.10         2.66        19.73 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       12.605                        15.580 
[1] "0.1 - 60.4 (12.6)"  "0.3 - 122.1 (15.6)"
[1] "hr=" "1.5"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         4        2        4        1        27
  DEL PEAK 11(4P15.2) WILD-TYPE       4        3        2        0        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          16        15          8          6
  DEL PEAK 11(4P15.2) WILD-TYPE        15        10          6          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(4P15.2) MUTATED            3        4         1
  DEL PEAK 11(4P15.2) WILD-TYPE          4        1         3
D41V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           27                            20
  STAGE IIB                           16                            15
  STAGE III                           15                            10
  STAGE IIIA                           8                             6
  STAGE IIIB                           6                             3
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 11(4P15.2) MUTATED      14 28 47  4
  DEL PEAK 11(4P15.2) WILD-TYPE    18 15 40  1
D41V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                          14                            18
  T2                             28                            15
  T3                             47                            40
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 11(4P15.2) MUTATED   43 38  8  4
  DEL PEAK 11(4P15.2) WILD-TYPE 34 30  4  4
D41V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                          43                            34
  N1                          38                            30
  N2                           8                             4
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   82  5
  DEL PEAK 11(4P15.2) WILD-TYPE 53  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     82    5
  DEL PEAK 11(4P15.2) WILD-TYPE   53    4
   clus
vv  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  0                          82                            53
  1                           5                             4
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   14 92
  DEL PEAK 11(4P15.2) WILD-TYPE 13 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     14   92
  DEL PEAK 11(4P15.2) WILD-TYPE   13   65
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          14                            13
  MALE                            92                            65
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   69 25
  DEL PEAK 11(4P15.2) WILD-TYPE 54 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     69   25
  DEL PEAK 11(4P15.2) WILD-TYPE   54   18
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                           69                            54
  YES                          25                            18
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   50 56
  DEL PEAK 11(4P15.2) WILD-TYPE 38 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     50   56
  DEL PEAK 11(4P15.2) WILD-TYPE   38   40
                                   clus
vv                                  DEL PEAK 11(4P15.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              50
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          56
                                   clus
vv                                  DEL PEAK 11(4P15.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                38
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            40
[1] 2 2
[1] FALSE
D41V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(4P15.2) MUTATED   79  9  1  2
  DEL PEAK 11(4P15.2) WILD-TYPE 58  3  1  5
D41V12, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  R0                          79                            58
  R1                           9                             3
  R2                           1                             1
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED      30                         2    61
  DEL PEAK 11(4P15.2) WILD-TYPE    16                         3    53
D41V14, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                              30
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              61
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED    3 54
  DEL PEAK 11(4P15.2) WILD-TYPE  3 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      3   54
  DEL PEAK 11(4P15.2) WILD-TYPE    3   34
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            34
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(4Q22.1) MUTATED   58 47
  DEL PEAK 12(4Q22.1) WILD-TYPE 50 29
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          105                            79 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           47                            29 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97        27.12        20.02        25.78        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L 
       32.45        33.27        35.21         0.85         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH 
        0.79        12.82         4.67        12.16        44.75        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       23.18        25.22         3.16         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       16.47        13.22         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.38        15.35        13.25        12.46        12.59        12.76 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.85        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        13.18        12.33        13.18        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
       16.44         9.27         8.98        27.09        22.82         1.55 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       28.11        52.27        18.05        11.24        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       14.37         3.42         2.66 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU 
       15.68        34.85        19.99        22.82         0.36         5.16 
TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       58.55         7.69        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        9.30        17.03        23.41         9.96        14.86        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
      122.10        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88W 
       21.01        47.93        18.35         7.17        29.00        25.12 
TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L7-A56G 
        3.02        13.55         7.76         5.49        21.37        10.85 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
       12.43        12.33        13.15        12.59        12.62        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HX 
       12.59        22.39        15.52        11.54        13.22        12.23 
TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.03        13.38         0.13        12.03        33.11         7.82 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       16.31        53.95         2.89         5.29         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       25.81        12.43        18.31         8.12        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       46.19         9.17        18.21        41.23         2.10         1.32 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.53                          0.13 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        12.69                         14.86 
[1] "0.5 - 83.2 (12.7)"  "0.1 - 122.1 (14.9)"
[1] "hr=" "1.4"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         2        1        5        1        23
  DEL PEAK 12(4Q22.1) WILD-TYPE       6        4        1        0        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          17        18          8          6
  DEL PEAK 12(4Q22.1) WILD-TYPE        14         7          6          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(4Q22.1) MUTATED            2        4         4
  DEL PEAK 12(4Q22.1) WILD-TYPE          5        1         0
D42V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             5                             1
  STAGE II                             1                             0
  STAGE IIA                           23                            24
  STAGE IIB                           17                            14
  STAGE III                           18                             7
  STAGE IIIA                           8                             6
  STAGE IIIB                           6                             3
  STAGE IIIC                           2                             5
  STAGE IV                             4                             1
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 12(4Q22.1) MUTATED      12 26 53  2
  DEL PEAK 12(4Q22.1) WILD-TYPE    20 17 34  3
D42V4, multiclass
       clus
vv      DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T0+T1                          12                            20
  T2                             26                            17
  T3                             53                            34
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 12(4Q22.1) MUTATED   38 43  9  3
  DEL PEAK 12(4Q22.1) WILD-TYPE 39 25  3  5
D42V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          38                            39
  N1                          43                            25
  N2                           9                             3
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   74  8
  DEL PEAK 12(4Q22.1) WILD-TYPE 61  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     74    8
  DEL PEAK 12(4Q22.1) WILD-TYPE   61    1
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                          74                            61
  1                           8                             1
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   12 93
  DEL PEAK 12(4Q22.1) WILD-TYPE 15 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     12   93
  DEL PEAK 12(4Q22.1) WILD-TYPE   15   64
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          12                            15
  MALE                            93                            64
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   71 21
  DEL PEAK 12(4Q22.1) WILD-TYPE 52 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     71   21
  DEL PEAK 12(4Q22.1) WILD-TYPE   52   22
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                           71                            52
  YES                          21                            22
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   59 46
  DEL PEAK 12(4Q22.1) WILD-TYPE 29 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     59   46
  DEL PEAK 12(4Q22.1) WILD-TYPE   29   50
                                   clus
vv                                  DEL PEAK 12(4Q22.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              59
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          46
                                   clus
vv                                  DEL PEAK 12(4Q22.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                29
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            50
[1] 2 2
[1] FALSE
D42V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 12(4Q22.1) MUTATED   78  8  2  3
  DEL PEAK 12(4Q22.1) WILD-TYPE 59  4  0  4
D42V12, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                          78                            59
  R1                           8                             4
  R2                           2                             0
  RX                           3                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED      27                         2    62
  DEL PEAK 12(4Q22.1) WILD-TYPE    19                         3    52
D42V14, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                              27
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              62
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED    4 47
  DEL PEAK 12(4Q22.1) WILD-TYPE  2 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4   47
  DEL PEAK 12(4Q22.1) WILD-TYPE    2   41
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            41
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(4Q34.3) MUTATED   53 46
  DEL PEAK 13(4Q34.3) WILD-TYPE 55 30
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           99                            85 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           46                            30 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GI 
        0.36        35.97        27.12         5.16        25.78        14.30 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
        5.92         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-JY-A6F8 
        0.85         3.88         0.53         0.79        12.82       122.10 
TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       44.75        41.52        47.38        23.18        25.22         3.16 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
        7.13         7.43        15.48         7.40         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
        2.66        12.92        16.47        13.22         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.41        83.24        46.09        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.66        13.41        13.38        13.25        12.59        12.76 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.85        12.33         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.23        13.18        12.33        13.38        12.85        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38        16.44         9.27         8.98        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55         8.12        28.11        18.18        52.27        18.05 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-ZR-A9CJ 
       15.91        25.08        19.73 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-S8-A6BV TCGA-2H-A9GH 
       15.68        34.85        19.99        22.82        20.02        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA 
       58.55         7.63        13.94         7.69        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12        18.64         9.30        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        9.96        14.86         4.67        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
        3.68        21.70        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ 
        0.30        26.33        32.61        21.01        47.93         1.38 
TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK 
       29.00         2.60        25.12         3.02        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49P 
        7.76        21.37        52.57        10.85        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35        12.59        12.62        12.46        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        22.39        15.52        11.54        13.22        25.25 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6L4 
       12.03        13.18         0.13        12.03        33.11        16.31 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
       53.95        15.78         5.29         3.42        15.35        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       12.43        18.31        33.70        46.19        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         0.36                          0.13 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       122.10                         68.02 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                        12.59                         14.50 
[1] "0.4 - 122.1 (12.6)" "0.1 - 68.0 (14.5)" 
[1] "hr=" "1.5"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q34.3) MUTATED         3        2        5        1        17
  DEL PEAK 13(4Q34.3) WILD-TYPE       5        3        1        0        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q34.3) MUTATED          14        17          6          8
  DEL PEAK 13(4Q34.3) WILD-TYPE        17         8          8          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(4Q34.3) MUTATED            4        3         3
  DEL PEAK 13(4Q34.3) WILD-TYPE          3        2         1
D43V3, multiclass
            clus
vv           DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             5                             1
  STAGE II                             1                             0
  STAGE IIA                           17                            30
  STAGE IIB                           14                            17
  STAGE III                           17                             8
  STAGE IIIA                           6                             8
  STAGE IIIB                           8                             1
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 13(4Q34.3) MUTATED      13 23 48  2
  DEL PEAK 13(4Q34.3) WILD-TYPE    19 20 39  3
D43V4, multiclass
       clus
vv      DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  T0+T1                          13                            19
  T2                             23                            20
  T3                             48                            39
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(4Q34.3) MUTATED   34 38 10  4
  DEL PEAK 13(4Q34.3) WILD-TYPE 43 30  2  4
D43V5, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  N0                          34                            43
  N1                          38                            30
  N2                          10                             2
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   68  6
  DEL PEAK 13(4Q34.3) WILD-TYPE 67  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     68    6
  DEL PEAK 13(4Q34.3) WILD-TYPE   67    3
   clus
vv  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  0                          68                            67
  1                           6                             3
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   12 87
  DEL PEAK 13(4Q34.3) WILD-TYPE 15 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     12   87
  DEL PEAK 13(4Q34.3) WILD-TYPE   15   70
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          12                            15
  MALE                            87                            70
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   66 18
  DEL PEAK 13(4Q34.3) WILD-TYPE 57 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     66   18
  DEL PEAK 13(4Q34.3) WILD-TYPE   57   25
     clus
vv    DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  NO                           66                            57
  YES                          18                            25
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   58 41
  DEL PEAK 13(4Q34.3) WILD-TYPE 30 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     58   41
  DEL PEAK 13(4Q34.3) WILD-TYPE   30   55
                                   clus
vv                                  DEL PEAK 13(4Q34.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          41
                                   clus
vv                                  DEL PEAK 13(4Q34.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            55
[1] 2 2
[1] FALSE
D43V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 13(4Q34.3) MUTATED   69  8  2  5
  DEL PEAK 13(4Q34.3) WILD-TYPE 68  4  0  2
D43V12, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  R0                          69                            68
  R1                           8                             4
  R2                           2                             0
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q34.3) MUTATED      25                         1    62
  DEL PEAK 13(4Q34.3) WILD-TYPE    21                         4    52
D43V14, multiclass
                           clus
vv                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              62
                           clus
vv                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED    3 42
  DEL PEAK 13(4Q34.3) WILD-TYPE  3 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      3   42
  DEL PEAK 13(4Q34.3) WILD-TYPE    3   46
                        clus
vv                       DEL PEAK 13(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK 13(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            46
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 14(5Q12.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(5Q12.1) MUTATED   64 48
  DEL PEAK 14(5Q12.1) WILD-TYPE 44 28
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          112                            72 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           48                            28 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.12         5.16        20.02        25.78        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS 
       32.45        33.27        35.21         0.85         2.63         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FH 
        0.53        17.03         4.67       122.10        44.75        47.38 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       31.56        25.22        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.13         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48        13.55         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45        12.43        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       13.25        12.46        12.49        22.39        15.52        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ 
       12.03        13.18        12.33        13.38        13.18        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.26        33.11         5.06        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-AASW 
        9.30         2.89         2.30        12.69         3.42         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        8.98        25.81        27.09        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
        8.12        28.11        52.27        11.24        15.91        25.08 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-2H-A9GH TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       31.27         7.69        20.78        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       12.16        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.03         6.28         3.16         0.30        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ 
       29.00         7.43        15.48        25.12         7.40        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       13.22         7.76        83.24        12.66        13.41        12.33 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.62        12.59        12.76        12.59        12.85        11.54 
TCGA-LN-A4MR TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.22         0.13        12.03         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       16.31         7.04        15.78         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       16.44        15.35         1.55        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05         9.17        18.21        41.23        14.37         3.42 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         0.36                          0.13 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       12.770                        13.315 
[1] "0.4 - 122.1 (12.8)" "0.1 - 83.2 (13.3)" 
[1] "hr=" "1"  
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         8        3        1        0        27
  DEL PEAK 14(5Q12.1) WILD-TYPE       0        2        5        1        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          15        18          8          6
  DEL PEAK 14(5Q12.1) WILD-TYPE        16         7          6          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(5Q12.1) MUTATED            4        5         3
  DEL PEAK 14(5Q12.1) WILD-TYPE          3        0         1
D44V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              8                             0
  STAGE IA                             3                             2
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           27                            20
  STAGE IIB                           15                            16
  STAGE III                           18                             7
  STAGE IIIA                           8                             6
  STAGE IIIB                           6                             3
  STAGE IIIC                           4                             3
  STAGE IV                             5                             0
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 14(5Q12.1) MUTATED      19 24 54  3
  DEL PEAK 14(5Q12.1) WILD-TYPE    13 19 33  2
D44V4, multiclass
       clus
vv      DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T0+T1                          19                            13
  T2                             24                            19
  T3                             54                            33
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 14(5Q12.1) MUTATED   46 43  6  5
  DEL PEAK 14(5Q12.1) WILD-TYPE 31 25  6  3
D44V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          46                            31
  N1                          43                            25
  N2                           6                             6
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   81  8
  DEL PEAK 14(5Q12.1) WILD-TYPE 54  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     81    8
  DEL PEAK 14(5Q12.1) WILD-TYPE   54    1
   clus
vv  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  0                          81                            54
  1                           8                             1
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   13 99
  DEL PEAK 14(5Q12.1) WILD-TYPE 14 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     13   99
  DEL PEAK 14(5Q12.1) WILD-TYPE   14   58
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          13                            14
  MALE                            99                            58
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   76 25
  DEL PEAK 14(5Q12.1) WILD-TYPE 47 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     76   25
  DEL PEAK 14(5Q12.1) WILD-TYPE   47   18
     clus
vv    DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  NO                           76                            47
  YES                          25                            18
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   58 54
  DEL PEAK 14(5Q12.1) WILD-TYPE 30 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     58   54
  DEL PEAK 14(5Q12.1) WILD-TYPE   30   42
                                   clus
vv                                  DEL PEAK 14(5Q12.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          54
                                   clus
vv                                  DEL PEAK 14(5Q12.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            42
[1] 2 2
[1] FALSE
D44V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 14(5Q12.1) MUTATED   82  9  2  5
  DEL PEAK 14(5Q12.1) WILD-TYPE 55  3  0  2
D44V12, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  R0                          82                            55
  R1                           9                             3
  R2                           2                             0
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q12.1) MUTATED      30                         3    64
  DEL PEAK 14(5Q12.1) WILD-TYPE    16                         2    50
D44V14, multiclass
                           clus
vv                          DEL PEAK 14(5Q12.1) MUTATED
  ASIAN                                              30
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              64
                           clus
vv                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED    3 50
  DEL PEAK 14(5Q12.1) WILD-TYPE  3 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      3   50
  DEL PEAK 14(5Q12.1) WILD-TYPE    3   38
                        clus
vv                       DEL PEAK 14(5Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK 14(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            38
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(6P25.3) MUTATED   40 34
  DEL PEAK 15(6P25.3) WILD-TYPE 68 42
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           74                           110 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           34                            42 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         4.31         4.70         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
        5.16        20.02        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        8.94         4.21        33.27        18.64         3.88         0.53 
TCGA-IG-A5S3 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
       23.41        12.16       122.10        23.18        31.56         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       30.25         0.30        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.16         7.13         2.66        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       13.22        13.41        52.57        10.36         5.92        12.43 
TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.33        12.59        13.25        12.49        12.33        25.25 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        12.33        13.38        12.85        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.59        16.31         9.30        15.78         2.89        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ER 
       20.38         5.29         3.42        15.35         9.27        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 
       18.31         8.12        18.18        18.05        11.24        25.08 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI 
       15.68        34.85        18.28         8.94        24.00        19.99 
TCGA-L5-A88T TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
       22.82        25.78        31.27         5.92        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OF 
       47.38        21.70        25.22        24.03         6.28        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       32.61        21.01        47.93        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.02        55.50        12.92         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        8.71        83.24        46.09        10.85        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        13.38        13.15        15.35        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW 
       12.23        12.03        13.18         0.13        12.03         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         5.06         7.04        38.40         6.35        53.95 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        2.30         7.00        16.44         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       22.82         1.55        28.11        33.70        52.27        46.19 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.30                          0.13 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                        12.64                         13.20 
[1] "0.3 - 122.1 (12.6)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.4"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(6P25.3) MUTATED         5        2        1        0        15
  DEL PEAK 15(6P25.3) WILD-TYPE       3        3        5        1        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED          13        11          4          4
  DEL PEAK 15(6P25.3) WILD-TYPE        18        14         10          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(6P25.3) MUTATED            5        2         2
  DEL PEAK 15(6P25.3) WILD-TYPE          2        3         2
D45V3, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           15                            32
  STAGE IIB                           13                            18
  STAGE III                           11                            14
  STAGE IIIA                           4                            10
  STAGE IIIB                           4                             5
  STAGE IIIC                           5                             2
  STAGE IV                             2                             3
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 15(6P25.3) MUTATED      13 15 37  1
  DEL PEAK 15(6P25.3) WILD-TYPE    19 28 50  4
D45V4, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T0+T1                          13                            19
  T2                             15                            28
  T3                             37                            50
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 15(6P25.3) MUTATED   30 24  6  6
  DEL PEAK 15(6P25.3) WILD-TYPE 47 44  6  2
D45V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          30                            47
  N1                          24                            44
  N2                           6                             6
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   50  4
  DEL PEAK 15(6P25.3) WILD-TYPE 85  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     50    4
  DEL PEAK 15(6P25.3) WILD-TYPE   85    5
   clus
vv  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  0                          50                            85
  1                           4                             5
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   10 64
  DEL PEAK 15(6P25.3) WILD-TYPE 17 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     10   64
  DEL PEAK 15(6P25.3) WILD-TYPE   17   93
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          10                            17
  MALE                            64                            93
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   47 18
  DEL PEAK 15(6P25.3) WILD-TYPE 76 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     47   18
  DEL PEAK 15(6P25.3) WILD-TYPE   76   25
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                           47                            76
  YES                          18                            25
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   41 33
  DEL PEAK 15(6P25.3) WILD-TYPE 47 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     41   33
  DEL PEAK 15(6P25.3) WILD-TYPE   47   63
                                   clus
vv                                  DEL PEAK 15(6P25.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              41
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          33
                                   clus
vv                                  DEL PEAK 15(6P25.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                47
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            63
[1] 2 2
[1] FALSE
D45V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(6P25.3) MUTATED   56  5  0  2
  DEL PEAK 15(6P25.3) WILD-TYPE 81  7  2  5
D45V12, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          56                            81
  R1                           5                             7
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED      16                         3    45
  DEL PEAK 15(6P25.3) WILD-TYPE    30                         2    69
D45V14, multiclass
                           clus
vv                          DEL PEAK 15(6P25.3) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              45
                           clus
vv                          DEL PEAK 15(6P25.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED    4 31
  DEL PEAK 15(6P25.3) WILD-TYPE  2 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      4   31
  DEL PEAK 15(6P25.3) WILD-TYPE    2   57
                        clus
vv                       DEL PEAK 15(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       DEL PEAK 15(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            57
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 16(6Q16.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(6Q16.3) MUTATED   34 21
  DEL PEAK 16(6Q16.3) WILD-TYPE 74 55
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           55                           129 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           21                            55 
$`DEL PEAK 16(6Q16.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GF TCGA-IC-A6RE 
       60.39         8.94         0.36        20.02        25.78         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       33.27        35.21         0.53         4.67        14.50        44.75 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A8NJ 
       47.38        25.22         3.16        18.35         3.16        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
       13.55        13.22        13.41        83.24        52.57         5.92 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       13.38        13.25        12.62        12.59        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       13.22        12.33        25.25        12.33        13.18         0.13 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG 
       12.26         8.02         5.06        38.40         2.89        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
       20.38         3.42         9.27        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        8.12        28.11        25.08        14.37         3.42         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`DEL PEAK 16(6Q16.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GH 
       19.99        22.82        35.97        27.12         5.16        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       16.24         4.21        32.45         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 
       23.41        12.82         9.96        14.86        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       21.01        47.93         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48         7.76         5.49        21.37         8.71 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       13.41        12.33        13.15        15.35        12.59        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.38        12.03        12.85        33.11         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        2.30         7.00         5.29        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       25.81        27.09         1.55        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23         1.32         2.66 

  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        13.22                         12.85 
[1] "0.1 - 83.2 (13.2)"  "0.3 - 122.1 (12.8)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6Q16.3) MUTATED         1        1        1        0        15
  DEL PEAK 16(6Q16.3) WILD-TYPE       7        4        5        1        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q16.3) MUTATED          10         8          4          2
  DEL PEAK 16(6Q16.3) WILD-TYPE        21        17         10          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(6Q16.3) MUTATED            1        1         1
  DEL PEAK 16(6Q16.3) WILD-TYPE          6        4         3
D46V3, multiclass
            clus
vv           DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             4
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           15                            32
  STAGE IIB                           10                            21
  STAGE III                            8                            17
  STAGE IIIA                           4                            10
  STAGE IIIB                           2                             7
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 16(6Q16.3) MUTATED       8 14 24  1
  DEL PEAK 16(6Q16.3) WILD-TYPE    24 29 63  4
D46V4, multiclass
       clus
vv      DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  T0+T1                           8                            24
  T2                             14                            29
  T3                             24                            63
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 16(6Q16.3) MUTATED   20 22  3  1
  DEL PEAK 16(6Q16.3) WILD-TYPE 57 46  9  7
D46V5, multiclass
    clus
vv   DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  N0                          20                            57
  N1                          22                            46
  N2                           3                             9
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED   38  2
  DEL PEAK 16(6Q16.3) WILD-TYPE 97  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED     38    2
  DEL PEAK 16(6Q16.3) WILD-TYPE   97    7
   clus
vv  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  0                          38                            97
  1                           2                             7
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6Q16.3) MUTATED     4  51
  DEL PEAK 16(6Q16.3) WILD-TYPE  23 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED      4   51
  DEL PEAK 16(6Q16.3) WILD-TYPE   23  106
        clus
vv       DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  FEMALE                           4                            23
  MALE                            51                           106
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED   32 14
  DEL PEAK 16(6Q16.3) WILD-TYPE 91 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED     32   14
  DEL PEAK 16(6Q16.3) WILD-TYPE   91   29
     clus
vv    DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  NO                           32                            91
  YES                          14                            29
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED   24 31
  DEL PEAK 16(6Q16.3) WILD-TYPE 64 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED     24   31
  DEL PEAK 16(6Q16.3) WILD-TYPE   64   65
                                   clus
vv                                  DEL PEAK 16(6Q16.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              24
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          31
                                   clus
vv                                  DEL PEAK 16(6Q16.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                64
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            65
[1] 2 2
[1] FALSE
D46V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 16(6Q16.3) MUTATED   40  4  0  2
  DEL PEAK 16(6Q16.3) WILD-TYPE 97  8  2  5
D46V12, multiclass
    clus
vv   DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  R0                          40                            97
  R1                           4                             8
  R2                           0                             2
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q16.3) MUTATED      19                         3    29
  DEL PEAK 16(6Q16.3) WILD-TYPE    27                         2    85
D46V14, multiclass
                           clus
vv                          DEL PEAK 16(6Q16.3) MUTATED
  ASIAN                                              19
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              29
                           clus
vv                          DEL PEAK 16(6Q16.3) WILD-TYPE
  ASIAN                                                27
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED    3 30
  DEL PEAK 16(6Q16.3) WILD-TYPE  3 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED      3   30
  DEL PEAK 16(6Q16.3) WILD-TYPE    3   58
                        clus
vv                       DEL PEAK 16(6Q16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       DEL PEAK 16(6Q16.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            58
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D47V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 17(6Q26) MUTATED   32 18
  DEL PEAK 17(6Q26) WILD-TYPE 76 58
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         50                         134 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         18                          58 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-2H-A9GF TCGA-IG-A3I8 
       34.85         4.31         8.94         0.36        25.78        33.27 
TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C 
       35.21         4.67        14.50        47.38        25.22         3.16 
TCGA-L5-A4OR TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.16         7.40        13.48        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       13.41        83.24        52.57         5.92        13.38        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       12.62        12.59        12.49        12.76        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-R6-A6DN 
       13.22        25.25        12.00        12.23        12.33         8.02 
TCGA-R6-A6XG TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
       38.40         2.30        12.69        20.38         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-XP-A8T6 
        9.27        22.82        12.43         8.12        28.11        25.08 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        18.28        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH 
       22.82        35.97        27.12         5.16        20.02        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        55.50         2.66        12.92         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       21.37         8.71        46.09        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.46        12.59        12.85        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
        4.47        12.33        10.52        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30        15.78         2.89         7.00         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35         8.98        25.81        27.09         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
        9.17        15.91        18.21        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       0.36                        0.13 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     13.220                      12.885 
[1] "0.4 - 83.2 (13.2)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1.2"
D47V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q26) MUTATED         0        1        2        0        17
  DEL PEAK 17(6Q26) WILD-TYPE       8        4        4        1        30
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           6        10          1          2
  DEL PEAK 17(6Q26) WILD-TYPE        25        15         13          7
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(6Q26) MUTATED            1        0         1
  DEL PEAK 17(6Q26) WILD-TYPE          6        5         3
D47V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            0                           8
  STAGE IA                           1                           4
  STAGE IB                           2                           4
  STAGE II                           0                           1
  STAGE IIA                         17                          30
  STAGE IIB                          6                          25
  STAGE III                         10                          15
  STAGE IIIA                         1                          13
  STAGE IIIB                         2                           7
  STAGE IIIC                         1                           6
  STAGE IV                           0                           5
  STAGE IVA                          1                           3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 17(6Q26) MUTATED       5 11 26  1
  DEL PEAK 17(6Q26) WILD-TYPE    27 32 61  4
D47V4, multiclass
       clus
vv      DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T0+T1                         5                          27
  T2                           11                          32
  T3                           26                          61
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 17(6Q26) MUTATED   23 15  3  1
  DEL PEAK 17(6Q26) WILD-TYPE 54 53  9  7
D47V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        23                          54
  N1                        15                          53
  N2                         3                           9
  N3                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED   36  1
  DEL PEAK 17(6Q26) WILD-TYPE 99  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     36    1
  DEL PEAK 17(6Q26) WILD-TYPE   99    8
   clus
vv  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  0                        36                          99
  1                         1                           8
[1] 2 2
[1] FALSE
D47V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     4  46
  DEL PEAK 17(6Q26) WILD-TYPE  23 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      4   46
  DEL PEAK 17(6Q26) WILD-TYPE   23  111
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                         4                          23
  MALE                          46                         111
[1] 2 2
[1] FALSE
D47V8, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED   28 13
  DEL PEAK 17(6Q26) WILD-TYPE 95 30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     28   13
  DEL PEAK 17(6Q26) WILD-TYPE   95   30
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                         28                          95
  YES                        13                          30
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED   22 28
  DEL PEAK 17(6Q26) WILD-TYPE 66 68
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     22   28
  DEL PEAK 17(6Q26) WILD-TYPE   66   68
                                   clus
vv                                  DEL PEAK 17(6Q26) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                            22
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                        28
                                   clus
vv                                  DEL PEAK 17(6Q26) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                              66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          68
[1] 2 2
[1] FALSE
D47V11, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    36   4   0   2
  DEL PEAK 17(6Q26) WILD-TYPE 101   8   2   5
D47V12, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        36                         101
  R1                         4                           8
  R2                         0                           2
  RX                         2                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED      17                         2    27
  DEL PEAK 17(6Q26) WILD-TYPE    29                         3    87
D47V14, multiclass
                           clus
vv                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                            17
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            27
                           clus
vv                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED    2 26
  DEL PEAK 17(6Q26) WILD-TYPE  4 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      2   26
  DEL PEAK 17(6Q26) WILD-TYPE    4   62
                        clus
vv                       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           4
  NOT HISPANIC OR LATINO                        26                          62
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 18(7Q31.1) MUTATED   28 28
  DEL PEAK 18(7Q31.1) WILD-TYPE 80 48
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           56                           128 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           28                            48 
$`DEL PEAK 18(7Q31.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A88Y TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       18.28         0.36        25.78        14.30         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94         4.21        32.45         7.69         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 
       20.12         3.88        17.03         0.79         9.96         4.67 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       47.38         3.16        26.33        47.93         3.16        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60        25.12        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N 
       13.48        16.47        13.55         8.71        10.36        12.43 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.38        13.25        12.62        12.46        12.76        12.85 
TCGA-LN-A4MR TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 
       13.22         0.13        33.11         5.06        15.78         2.89 
TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7D 
        5.29         8.98        22.82         1.55        18.05         9.17 
TCGA-VR-AA7I TCGA-Z6-AAPN 
       15.91         2.66 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A3I8 
       20.02        31.27        58.55        13.94        16.24        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 
       35.21        20.78        18.64         9.30         0.53        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       25.22        24.03         6.28        30.25         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       21.01        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.13         7.43         7.40         3.75         3.02 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       13.41        12.33        13.15        15.35        12.59        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.49        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38        13.18        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.85        12.26         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC 
        7.04        38.40         6.35        53.95         9.30         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        27.09        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        1.32        19.73 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         55.5                         122.1 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        12.54                         13.30 
[1] "0.1 - 55.5 (12.5)"  "0.3 - 122.1 (13.3)"
[1] "hr=" "1.9"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(7Q31.1) MUTATED         0        2        2        1        11
  DEL PEAK 18(7Q31.1) WILD-TYPE       8        3        4        0        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           7        15          5          2
  DEL PEAK 18(7Q31.1) WILD-TYPE        24        10          9          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(7Q31.1) MUTATED            2        1         2
  DEL PEAK 18(7Q31.1) WILD-TYPE          5        4         2
D48V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             2                             3
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                           11                            36
  STAGE IIB                            7                            24
  STAGE III                           15                            10
  STAGE IIIA                           5                             9
  STAGE IIIB                           2                             7
  STAGE IIIC                           2                             5
  STAGE IV                             1                             4
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 18(7Q31.1) MUTATED       9  9 32  2
  DEL PEAK 18(7Q31.1) WILD-TYPE    23 34 55  3
D48V4, multiclass
       clus
vv      DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T0+T1                           9                            23
  T2                              9                            34
  T3                             32                            55
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 18(7Q31.1) MUTATED   21 26  3  2
  DEL PEAK 18(7Q31.1) WILD-TYPE 56 42  9  6
D48V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                          21                            56
  N1                          26                            42
  N2                           3                             9
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED   39  3
  DEL PEAK 18(7Q31.1) WILD-TYPE 96  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     39    3
  DEL PEAK 18(7Q31.1) WILD-TYPE   96    6
   clus
vv  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  0                          39                            96
  1                           3                             6
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     4  52
  DEL PEAK 18(7Q31.1) WILD-TYPE  23 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      4   52
  DEL PEAK 18(7Q31.1) WILD-TYPE   23  105
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           4                            23
  MALE                            52                           105
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED   41 10
  DEL PEAK 18(7Q31.1) WILD-TYPE 82 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     41   10
  DEL PEAK 18(7Q31.1) WILD-TYPE   82   33
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                           41                            82
  YES                          10                            33
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED   31 25
  DEL PEAK 18(7Q31.1) WILD-TYPE 57 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     31   25
  DEL PEAK 18(7Q31.1) WILD-TYPE   57   71
                                   clus
vv                                  DEL PEAK 18(7Q31.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          25
                                   clus
vv                                  DEL PEAK 18(7Q31.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                57
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            71
[1] 2 2
[1] FALSE
D48V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 18(7Q31.1) MUTATED   42  6  1  1
  DEL PEAK 18(7Q31.1) WILD-TYPE 95  6  1  6
D48V12, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          42                            95
  R1                           6                             6
  R2                           1                             1
  RX                           1                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(7Q31.1) MUTATED      10                         0    35
  DEL PEAK 18(7Q31.1) WILD-TYPE    36                         5    79
D48V14, multiclass
                           clus
vv                          DEL PEAK 18(7Q31.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              35
                           clus
vv                          DEL PEAK 18(7Q31.1) WILD-TYPE
  ASIAN                                                36
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED    1 23
  DEL PEAK 18(7Q31.1) WILD-TYPE  5 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      1   23
  DEL PEAK 18(7Q31.1) WILD-TYPE    5   65
                        clus
vv                       DEL PEAK 18(7Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       DEL PEAK 18(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            65
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 19(7Q36.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 19(7Q36.3) MUTATED   37 30
  DEL PEAK 19(7Q36.3) WILD-TYPE 71 46
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           67                           117 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           30                            46 
$`DEL PEAK 19(7Q36.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A88Y TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       18.28         0.36        25.78        14.30         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YC 
        8.94        16.24         4.21         7.69         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA 
       18.64        17.03         0.79         9.96        14.50        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF 
       68.02         3.68        47.38        25.22         3.16        26.33 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       47.93        18.35         7.17         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.13        15.48        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R 
       13.55         8.71        10.36        10.45        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15        12.62        12.46        12.59        12.76        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ 
       12.33        13.22        25.25        33.11         7.82         5.06 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
       38.40        15.78         5.29         8.98        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
        1.55        18.05        11.24         9.17        15.91         3.42 
TCGA-Z6-AAPN 
        2.66 

$`DEL PEAK 19(7Q36.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       20.02        31.27        58.55        13.94        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       35.21        20.78         2.63         3.88         9.30         0.53 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       23.41        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ 
       30.25         0.30        32.61        21.01         3.32         1.38 
TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.02        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.66        12.43        12.33        15.35        12.59        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
       12.49        12.59        22.39        15.52        11.54         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
       12.26         8.02         7.59        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP 
       20.38         3.42        16.44        15.35         9.27        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       52.27        46.19        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        2.10         1.32        19.73 

  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                         0.36                          0.13 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        12.85                         13.18 
[1] "0.4 - 68.0 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(7Q36.3) MUTATED         0        3        2        1        16
  DEL PEAK 19(7Q36.3) WILD-TYPE       8        2        4        0        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(7Q36.3) MUTATED          12        14          5          1
  DEL PEAK 19(7Q36.3) WILD-TYPE        19        11          9          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(7Q36.3) MUTATED            2        2         3
  DEL PEAK 19(7Q36.3) WILD-TYPE          5        3         1
D49V3, multiclass
            clus
vv           DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             3                             2
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                           16                            31
  STAGE IIB                           12                            19
  STAGE III                           14                            11
  STAGE IIIA                           5                             9
  STAGE IIIB                           1                             8
  STAGE IIIC                           2                             5
  STAGE IV                             2                             3
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 19(7Q36.3) MUTATED      11 13 36  3
  DEL PEAK 19(7Q36.3) WILD-TYPE    21 30 51  2
D49V4, multiclass
       clus
vv      DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  T0+T1                          11                            21
  T2                             13                            30
  T3                             36                            51
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 19(7Q36.3) MUTATED   27 30  2  3
  DEL PEAK 19(7Q36.3) WILD-TYPE 50 38 10  5
D49V5, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  N0                          27                            50
  N1                          30                            38
  N2                           2                            10
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED   48  5
  DEL PEAK 19(7Q36.3) WILD-TYPE 87  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED     48    5
  DEL PEAK 19(7Q36.3) WILD-TYPE   87    4
   clus
vv  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  0                          48                            87
  1                           5                             4
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED    9 58
  DEL PEAK 19(7Q36.3) WILD-TYPE 18 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      9   58
  DEL PEAK 19(7Q36.3) WILD-TYPE   18   99
        clus
vv       DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  FEMALE                           9                            18
  MALE                            58                            99
[1] 2 2
[1] FALSE
D49V8, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED   48 12
  DEL PEAK 19(7Q36.3) WILD-TYPE 75 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED     48   12
  DEL PEAK 19(7Q36.3) WILD-TYPE   75   31
     clus
vv    DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  NO                           48                            75
  YES                          12                            31
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED   33 34
  DEL PEAK 19(7Q36.3) WILD-TYPE 55 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED     33   34
  DEL PEAK 19(7Q36.3) WILD-TYPE   55   62
                                   clus
vv                                  DEL PEAK 19(7Q36.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              33
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          34
                                   clus
vv                                  DEL PEAK 19(7Q36.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                55
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            62
[1] 2 2
[1] FALSE
D49V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 19(7Q36.3) MUTATED   52  6  1  2
  DEL PEAK 19(7Q36.3) WILD-TYPE 85  6  1  5
D49V12, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  R0                          52                            85
  R1                           6                             6
  R2                           1                             1
  RX                           2                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(7Q36.3) MUTATED      15                         0    39
  DEL PEAK 19(7Q36.3) WILD-TYPE    31                         5    75
D49V14, multiclass
                           clus
vv                          DEL PEAK 19(7Q36.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              39
                           clus
vv                          DEL PEAK 19(7Q36.3) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED    1 28
  DEL PEAK 19(7Q36.3) WILD-TYPE  5 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      1   28
  DEL PEAK 19(7Q36.3) WILD-TYPE    5   60
                        clus
vv                       DEL PEAK 19(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          28
                        clus
vv                       DEL PEAK 19(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            60
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 20(8P23.2) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(8P23.2) MUTATED   57 35
  DEL PEAK 20(8P23.2) WILD-TYPE 51 41
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           92                            92 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           35                            41 
$`DEL PEAK 20(8P23.2) MUTATED`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM 
       27.12         5.16        25.78        31.27         5.92        13.94 
TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        4.21         0.85         2.63        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA 
       17.03         0.79        23.41         9.96        14.50        44.75 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        47.38        23.18        31.56        25.22        24.03 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V 
       26.33        32.61         3.32         4.90         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NN 
       25.12         7.40         3.75         2.66        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.43        13.15        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        22.39        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.00        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BW 
       12.26         7.82         8.02        53.95         2.30        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ER 
        5.29         3.42        16.44        15.35         9.27        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
       18.31         8.12        28.11        33.70        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE 
       11.24         9.17        15.91        25.08        41.23         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

$`DEL PEAK 20(8P23.2) WILD-TYPE`
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
        8.94         4.70        19.99        22.82         0.36        35.97 
TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       20.02        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45         7.69        33.27        35.21        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
        9.30        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       68.02        41.52        21.70         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        0.30        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A893 
        3.16        58.59        29.00         7.13        15.48         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
       55.50        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O 
       21.37        83.24        52.57        46.09         5.92        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 
       12.33        13.38        15.35        12.59        12.62        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.85        15.52        11.54         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        13.18        13.38        33.11         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        2.89        12.69         7.00         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T8 
       22.82         1.55        18.18        46.19        18.21        14.37 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                       12.540                        13.445 
[1] "0.1 - 60.4 (12.5)"  "0.3 - 122.1 (13.4)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(8P23.2) MUTATED         2        1        4        0        21
  DEL PEAK 20(8P23.2) WILD-TYPE       6        4        2        1        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P23.2) MUTATED          19        13          9          6
  DEL PEAK 20(8P23.2) WILD-TYPE        12        12          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(8P23.2) MUTATED            4        3         2
  DEL PEAK 20(8P23.2) WILD-TYPE          3        2         2
D50V3, multiclass
            clus
vv           DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             4                             2
  STAGE II                             0                             1
  STAGE IIA                           21                            26
  STAGE IIB                           19                            12
  STAGE III                           13                            12
  STAGE IIIA                           9                             5
  STAGE IIIB                           6                             3
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 20(8P23.2) MUTATED      13 24 46  3
  DEL PEAK 20(8P23.2) WILD-TYPE    19 19 41  2
D50V4, multiclass
       clus
vv      DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  T0+T1                          13                            19
  T2                             24                            19
  T3                             46                            41
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 20(8P23.2) MUTATED   35 38  7  5
  DEL PEAK 20(8P23.2) WILD-TYPE 42 30  5  3
D50V5, multiclass
    clus
vv   DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  N0                          35                            42
  N1                          38                            30
  N2                           7                             5
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED   71  5
  DEL PEAK 20(8P23.2) WILD-TYPE 64  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED     71    5
  DEL PEAK 20(8P23.2) WILD-TYPE   64    4
   clus
vv  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  0                          71                            64
  1                           5                             4
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED   12 80
  DEL PEAK 20(8P23.2) WILD-TYPE 15 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED     12   80
  DEL PEAK 20(8P23.2) WILD-TYPE   15   77
        clus
vv       DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  FEMALE                          12                            15
  MALE                            80                            77
[1] 2 2
[1] FALSE
D50V8, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED   57 27
  DEL PEAK 20(8P23.2) WILD-TYPE 66 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED     57   27
  DEL PEAK 20(8P23.2) WILD-TYPE   66   16
     clus
vv    DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  NO                           57                            66
  YES                          27                            16
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED   35 57
  DEL PEAK 20(8P23.2) WILD-TYPE 53 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED     35   57
  DEL PEAK 20(8P23.2) WILD-TYPE   53   39
                                   clus
vv                                  DEL PEAK 20(8P23.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              35
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          57
                                   clus
vv                                  DEL PEAK 20(8P23.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                53
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            39
[1] 2 2
[1] FALSE
D50V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 20(8P23.2) MUTATED   68  7  1  6
  DEL PEAK 20(8P23.2) WILD-TYPE 69  5  1  1
D50V12, multiclass
    clus
vv   DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  R0                          68                            69
  R1                           7                             5
  R2                           1                             1
  RX                           6                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P23.2) MUTATED      26                         4    52
  DEL PEAK 20(8P23.2) WILD-TYPE    20                         1    62
D50V14, multiclass
                           clus
vv                          DEL PEAK 20(8P23.2) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              52
                           clus
vv                          DEL PEAK 20(8P23.2) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED    3 46
  DEL PEAK 20(8P23.2) WILD-TYPE  3 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED      3   46
  DEL PEAK 20(8P23.2) WILD-TYPE    3   42
                        clus
vv                       DEL PEAK 20(8P23.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK 20(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            42
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 21(8P12) MUTATION ANALYSIS
D51V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 21(8P12) MUTATED   44 31
  DEL PEAK 21(8P12) WILD-TYPE 64 45
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         75                         109 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         31                          45 
$`DEL PEAK 21(8P12) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A8NT 
       60.39        34.85        18.28         4.31        24.00        27.12 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        31.27         5.92        13.94         4.21         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12        18.64         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C 
       23.41         9.96        14.50        44.75        47.38        23.18 
TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z 
       25.22        32.61        21.01         3.32         7.43         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR 
        3.75        55.50         2.66        13.48         5.49         8.71 
TCGA-L5-A8NS TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W 
       13.41        10.85        10.45        12.43        13.15        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.49        22.39        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ 
        4.47        12.33        12.00        12.33        13.18        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A8WC TCGA-RE-A7BO 
       12.26         7.82         8.02        38.40         2.30         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 
        5.29         3.42        16.44        18.31        28.11        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

$`DEL PEAK 21(8P12) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68         8.94         4.70        19.99        22.82         0.36 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       35.97         5.16        20.02        14.30        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        8.94        16.24        32.45        33.27        35.21        20.78 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        3.88         9.30        17.03        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       26.33        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       25.12         3.02        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        7.76        21.37        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
        5.92        12.66        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.59        12.62        12.59        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       15.52        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.38         0.13        12.03        33.11         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        2.89        12.69        20.38        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD 
       33.70        18.18        46.19        18.21        14.37         3.42 
TCGA-Z6-A9VB 
        1.32 

  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                       0.53                        0.13 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                      60.39                      122.10 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                      12.49                       13.22 
[1] "0.5 - 60.4 (12.5)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D51V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(8P12) MUTATED         3        0        2        0        15
  DEL PEAK 21(8P12) WILD-TYPE       5        5        4        1        32
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8P12) MUTATED          19         9          9          3
  DEL PEAK 21(8P12) WILD-TYPE        12        16          5          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(8P12) MUTATED            3        3         2
  DEL PEAK 21(8P12) WILD-TYPE          4        2         2
D51V3, multiclass
            clus
vv           DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  STAGE I                            3                           5
  STAGE IA                           0                           5
  STAGE IB                           2                           4
  STAGE II                           0                           1
  STAGE IIA                         15                          32
  STAGE IIB                         19                          12
  STAGE III                          9                          16
  STAGE IIIA                         9                           5
  STAGE IIIB                         3                           6
  STAGE IIIC                         3                           4
  STAGE IV                           3                           2
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 21(8P12) MUTATED      13 19 36  2
  DEL PEAK 21(8P12) WILD-TYPE    19 24 51  3
D51V4, multiclass
       clus
vv      DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  T0+T1                        13                          19
  T2                           19                          24
  T3                           36                          51
  T4                            2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 21(8P12) MUTATED   26 35  4  4
  DEL PEAK 21(8P12) WILD-TYPE 51 33  8  4
D51V5, multiclass
    clus
vv   DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  N0                        26                          51
  N1                        35                          33
  N2                         4                           8
  N3                         4                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED   60  5
  DEL PEAK 21(8P12) WILD-TYPE 75  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED     60    5
  DEL PEAK 21(8P12) WILD-TYPE   75    4
   clus
vv  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  0                        60                          75
  1                         5                           4
[1] 2 2
[1] FALSE
D51V7, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED    9 66
  DEL PEAK 21(8P12) WILD-TYPE 18 91
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED      9   66
  DEL PEAK 21(8P12) WILD-TYPE   18   91
        clus
vv       DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  FEMALE                         9                          18
  MALE                          66                          91
[1] 2 2
[1] FALSE
D51V8, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED   50 18
  DEL PEAK 21(8P12) WILD-TYPE 73 25
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED     50   18
  DEL PEAK 21(8P12) WILD-TYPE   73   25
     clus
vv    DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  NO                         50                          73
  YES                        18                          25
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED   33 42
  DEL PEAK 21(8P12) WILD-TYPE 55 54
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED     33   42
  DEL PEAK 21(8P12) WILD-TYPE   55   54
                                   clus
vv                                  DEL PEAK 21(8P12) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                            33
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                        42
                                   clus
vv                                  DEL PEAK 21(8P12) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                              55
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          54
[1] 2 2
[1] FALSE
D51V11, continuous
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK 21(8P12) MUTATED   58  4  2  4
  DEL PEAK 21(8P12) WILD-TYPE 79  8  0  3
D51V12, multiclass
    clus
vv   DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  R0                        58                          79
  R1                         4                           8
  R2                         2                           0
  RX                         4                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P12) MUTATED      21                         3    42
  DEL PEAK 21(8P12) WILD-TYPE    25                         2    72
D51V14, multiclass
                           clus
vv                          DEL PEAK 21(8P12) MUTATED
  ASIAN                                            21
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            42
                           clus
vv                          DEL PEAK 21(8P12) WILD-TYPE
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED    3 37
  DEL PEAK 21(8P12) WILD-TYPE  3 51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED      3   37
  DEL PEAK 21(8P12) WILD-TYPE    3   51
                        clus
vv                       DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  HISPANIC OR LATINO                             3                           3
  NOT HISPANIC OR LATINO                        37                          51
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 22(9P23) MUTATION ANALYSIS
D52V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 22(9P23) MUTATED   66 42
  DEL PEAK 22(9P23) WILD-TYPE 42 34
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        108                          76 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         42                          34 
$`DEL PEAK 22(9P23) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-Q9-A6FU 
       60.39        34.85        18.28         8.94        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN 
       20.02        25.78        31.27        14.30         7.63         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         4.21        32.45         7.69        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        3.88         0.53         0.79        23.41         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       12.16        44.75        68.02        31.56        25.22         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30        26.33        32.61        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59         7.13         7.43        15.48         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.75        55.50         2.66        13.48        16.47        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P 
        8.71        13.41        83.24        10.45        12.66        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.38        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.49        12.76        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       12.03        12.33         0.13        12.03        12.26        33.11 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        5.06        38.40         6.35         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       12.69        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR 
       18.31         8.12        28.11        52.27        46.19        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         1.32         2.66        19.73 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 
        0.36        27.12        58.55         5.92        13.94        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
       35.21         0.85        20.78         2.63         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       12.82         9.96        14.86       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       47.38        21.70        23.18        24.03         6.28        30.25 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88W 
       21.01        47.93         1.38         4.90        29.00        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
        7.40         3.02        12.92        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       21.37        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 
       12.43        13.41        13.15        12.59        12.59        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW 
        4.47        13.18        13.38        13.18        12.85         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 
        8.02         7.59        16.31         7.04        53.95         2.89 
TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        7.00        15.35        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE 
        9.17        15.91        25.08         2.10 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       0.13                        0.36 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                     12.725                      13.180 
[1] "0.1 - 83.2 (12.7)"  "0.4 - 122.1 (13.2)"
[1] "hr=" "1.1"
D52V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(9P23) MUTATED         2        2        4        1        28
  DEL PEAK 22(9P23) WILD-TYPE       6        3        2        0        19
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P23) MUTATED          18        19          7          5
  DEL PEAK 22(9P23) WILD-TYPE        13         6          7          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(9P23) MUTATED            3        1         4
  DEL PEAK 22(9P23) WILD-TYPE          4        4         0
D52V3, multiclass
            clus
vv           DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           2                           3
  STAGE IB                           4                           2
  STAGE II                           1                           0
  STAGE IIA                         28                          19
  STAGE IIB                         18                          13
  STAGE III                         19                           6
  STAGE IIIA                         7                           7
  STAGE IIIB                         5                           4
  STAGE IIIC                         3                           4
  STAGE IV                           1                           4
  STAGE IVA                          4                           0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 22(9P23) MUTATED      16 27 54  1
  DEL PEAK 22(9P23) WILD-TYPE    16 16 33  4
D52V4, multiclass
       clus
vv      DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T0+T1                        16                          16
  T2                           27                          16
  T3                           54                          33
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 22(9P23) MUTATED   41 47  6  3
  DEL PEAK 22(9P23) WILD-TYPE 36 21  6  5
D52V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                        41                          36
  N1                        47                          21
  N2                         6                           6
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   80  5
  DEL PEAK 22(9P23) WILD-TYPE 55  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     80    5
  DEL PEAK 22(9P23) WILD-TYPE   55    4
   clus
vv  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  0                        80                          55
  1                         5                           4
[1] 2 2
[1] FALSE
D52V7, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   10 98
  DEL PEAK 22(9P23) WILD-TYPE 17 59
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     10   98
  DEL PEAK 22(9P23) WILD-TYPE   17   59
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                        10                          17
  MALE                          98                          59
[1] 2 2
[1] FALSE
D52V8, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   68 29
  DEL PEAK 22(9P23) WILD-TYPE 55 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     68   29
  DEL PEAK 22(9P23) WILD-TYPE   55   14
     clus
vv    DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  NO                         68                          55
  YES                        29                          14
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   54 54
  DEL PEAK 22(9P23) WILD-TYPE 34 42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     54   54
  DEL PEAK 22(9P23) WILD-TYPE   34   42
                                   clus
vv                                  DEL PEAK 22(9P23) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                            54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                        54
                                   clus
vv                                  DEL PEAK 22(9P23) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                              34
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          42
[1] 2 2
[1] FALSE
D52V11, continuous
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK 22(9P23) MUTATED   84  6  0  2
  DEL PEAK 22(9P23) WILD-TYPE 53  6  2  5
D52V12, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  R0                        84                          53
  R1                         6                           6
  R2                         0                           2
  RX                         2                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P23) MUTATED      32                         2    59
  DEL PEAK 22(9P23) WILD-TYPE    14                         3    55
D52V14, multiclass
                           clus
vv                          DEL PEAK 22(9P23) MUTATED
  ASIAN                                            32
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            59
                           clus
vv                          DEL PEAK 22(9P23) WILD-TYPE
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED    5 52
  DEL PEAK 22(9P23) WILD-TYPE  1 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED      5   52
  DEL PEAK 22(9P23) WILD-TYPE    1   36
                        clus
vv                       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  HISPANIC OR LATINO                             5                           1
  NOT HISPANIC OR LATINO                        52                          36
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 23(9P21.3) MUTATED   85 56
  DEL PEAK 23(9P21.3) WILD-TYPE 23 20
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          141                            43 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           56                            20 
$`DEL PEAK 23(9P21.3) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y 
       60.39        34.85        18.28         4.31         8.94         0.36 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A93C 
        9.96         4.67        14.50        12.16        44.75        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       25.22         3.16         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         7.17        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43        15.48         2.60         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G 
        5.49        21.37         8.71        13.41        83.24        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       12.26        33.11         7.82         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        6.35         9.30        15.78         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        24.00         4.70        19.99        22.82        27.12 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A4QT TCGA-IG-A7DP 
       58.55         5.92        13.94        35.21         9.30        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OQ 
       31.56        24.03         6.28        30.25        21.01         1.38 
TCGA-L5-A4OR TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NV 
        3.16        25.12         7.40        13.48         7.76        52.57 
TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A8I1 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       46.09        12.59        13.18         8.02         7.59         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY 
       53.95         2.89         7.00        15.35        27.09        33.70 
TCGA-VR-A8Q7 
       52.27 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                         0.13                          1.38 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                        12.66                         19.99 
[1] "0.1 - 83.2 (12.7)"  "1.4 - 122.1 (20.0)"
[1] "hr=" "1.3"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P21.3) MUTATED         3        2        4        1        38
  DEL PEAK 23(9P21.3) WILD-TYPE       5        3        2        0         9
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P21.3) MUTATED          23        21         11          7
  DEL PEAK 23(9P21.3) WILD-TYPE         8         4          3          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(9P21.3) MUTATED            5        5         4
  DEL PEAK 23(9P21.3) WILD-TYPE          2        0         0
D53V3, multiclass
            clus
vv           DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           38                             9
  STAGE IIB                           23                             8
  STAGE III                           21                             4
  STAGE IIIA                          11                             3
  STAGE IIIB                           7                             2
  STAGE IIIC                           5                             2
  STAGE IV                             5                             0
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 23(9P21.3) MUTATED      20 34 71  4
  DEL PEAK 23(9P21.3) WILD-TYPE    12  9 16  1
D53V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          20                            12
  T2                             34                             9
  T3                             71                            16
  T4                              4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 23(9P21.3) MUTATED   58 55  9  6
  DEL PEAK 23(9P21.3) WILD-TYPE 19 13  3  2
D53V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                          58                            19
  N1                          55                            13
  N2                           9                             3
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED   104   9
  DEL PEAK 23(9P21.3) WILD-TYPE  31   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED    104    9
  DEL PEAK 23(9P21.3) WILD-TYPE   31    0
   clus
vv  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  0                         104                            31
  1                           9                             0
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    15 126
  DEL PEAK 23(9P21.3) WILD-TYPE  12  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     15  126
  DEL PEAK 23(9P21.3) WILD-TYPE   12   31
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          15                            12
  MALE                           126                            31
[1] 2 2
[1] FALSE
D53V8, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED   90 35
  DEL PEAK 23(9P21.3) WILD-TYPE 33  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     90   35
  DEL PEAK 23(9P21.3) WILD-TYPE   33    8
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  NO                           90                            33
  YES                          35                             8
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED   61 80
  DEL PEAK 23(9P21.3) WILD-TYPE 27 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     61   80
  DEL PEAK 23(9P21.3) WILD-TYPE   27   16
                                   clus
vv                                  DEL PEAK 23(9P21.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          80
                                   clus
vv                                  DEL PEAK 23(9P21.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                27
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            16
[1] 2 2
[1] FALSE
D53V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 23(9P21.3) MUTATED   105   9   2   6
  DEL PEAK 23(9P21.3) WILD-TYPE  32   3   0   1
D53V12, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  R0                         105                            32
  R1                           9                             3
  R2                           2                             0
  RX                           6                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P21.3) MUTATED      43                         4    78
  DEL PEAK 23(9P21.3) WILD-TYPE     3                         1    36
D53V14, multiclass
                           clus
vv                          DEL PEAK 23(9P21.3) MUTATED
  ASIAN                                              43
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              78
                           clus
vv                          DEL PEAK 23(9P21.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED    6 74
  DEL PEAK 23(9P21.3) WILD-TYPE  0 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED      6   74
  DEL PEAK 23(9P21.3) WILD-TYPE    0   14
                        clus
vv                       DEL PEAK 23(9P21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          74
                        clus
vv                       DEL PEAK 23(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            14
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 24(10P15.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(10P15.3) MUTATED   31 23
  DEL PEAK 24(10P15.3) WILD-TYPE 77 53
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            54                            130 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            23                             53 
$`DEL PEAK 24(10P15.3) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-2H-A9GF 
        4.31         8.94        24.00         4.70        27.12        25.78 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4P3 
       14.30         5.92         4.21        33.27         0.85        18.64 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43H 
        0.53         0.79        23.41        14.50        23.18         0.30 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NS TCGA-L5-A8NU 
        3.32         3.16         4.90         2.60        13.41        83.24 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A9 
       10.85         5.92        13.41        13.25        22.39        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        13.22         4.47        25.25        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       12.33        13.38         0.13        12.85        12.26         7.82 
TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EW TCGA-VR-A8EZ 
       53.95         5.29         3.42        16.44         8.12        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       18.05        11.24        25.08        14.37         3.42         2.66 

$`DEL PEAK 24(10P15.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ 
        0.36        35.97         5.16        20.02        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63        13.94         8.94        16.24        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       35.21        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 
       12.49        12.76        12.59        12.85        15.52        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18        12.03        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        7.00        20.38        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        52.27        46.19         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23         2.10         1.32        19.73 

  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          0.13                           0.36 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                        12.295                         13.300 
[1] "0.1 - 83.2 (12.3)"  "0.4 - 122.1 (13.3)"
[1] "hr=" "1.5"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(10P15.3) MUTATED         1        1        2        0        15
  DEL PEAK 24(10P15.3) WILD-TYPE       7        4        4        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10P15.3) MUTATED           9         9          3          4
  DEL PEAK 24(10P15.3) WILD-TYPE        22        16         11          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(10P15.3) MUTATED            2        3         0
  DEL PEAK 24(10P15.3) WILD-TYPE          5        2         4
D54V3, multiclass
            clus
vv           DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            15                             32
  STAGE IIB                             9                             22
  STAGE III                             9                             16
  STAGE IIIA                            3                             11
  STAGE IIIB                            4                              5
  STAGE IIIC                            2                              5
  STAGE IV                              3                              2
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 24(10P15.3) MUTATED       5 13 32  1
  DEL PEAK 24(10P15.3) WILD-TYPE    27 30 55  4
D54V4, multiclass
       clus
vv      DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  T0+T1                            5                             27
  T2                              13                             30
  T3                              32                             55
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 24(10P15.3) MUTATED   24 17  6  3
  DEL PEAK 24(10P15.3) WILD-TYPE 53 51  6  5
D54V5, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  N0                           24                             53
  N1                           17                             51
  N2                            6                              6
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED   42  3
  DEL PEAK 24(10P15.3) WILD-TYPE 93  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     42    3
  DEL PEAK 24(10P15.3) WILD-TYPE   93    6
   clus
vv  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  0                           42                             93
  1                            3                              6
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED     6  48
  DEL PEAK 24(10P15.3) WILD-TYPE  21 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      6   48
  DEL PEAK 24(10P15.3) WILD-TYPE   21  109
        clus
vv       DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  FEMALE                            6                             21
  MALE                             48                            109
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED   38 11
  DEL PEAK 24(10P15.3) WILD-TYPE 85 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     38   11
  DEL PEAK 24(10P15.3) WILD-TYPE   85   32
     clus
vv    DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  NO                            38                             85
  YES                           11                             32
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED   19 35
  DEL PEAK 24(10P15.3) WILD-TYPE 69 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     19   35
  DEL PEAK 24(10P15.3) WILD-TYPE   69   61
                                   clus
vv                                  DEL PEAK 24(10P15.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               19
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           35
                                   clus
vv                                  DEL PEAK 24(10P15.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             61
[1] 2 2
[1] FALSE
D54V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10P15.3) MUTATED    37   6   1   4
  DEL PEAK 24(10P15.3) WILD-TYPE 100   6   1   3
D54V12, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  R0                           37                            100
  R1                            6                              6
  R2                            1                              1
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10P15.3) MUTATED      20                         4    24
  DEL PEAK 24(10P15.3) WILD-TYPE    26                         1    90
D54V14, multiclass
                           clus
vv                          DEL PEAK 24(10P15.3) MUTATED
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               24
                           clus
vv                          DEL PEAK 24(10P15.3) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED    3 29
  DEL PEAK 24(10P15.3) WILD-TYPE  3 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      3   29
  DEL PEAK 24(10P15.3) WILD-TYPE    3   59
                        clus
vv                       DEL PEAK 24(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 24(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             59
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 25(10P11.21) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(10P11.21) MUTATED   29 23
  DEL PEAK 25(10P11.21) WILD-TYPE 79 53
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             52                             132 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             23                              53 
$`DEL PEAK 25(10P11.21) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-2H-A9GI TCGA-2H-A9GL 
        4.31        24.00         4.70        27.12        14.30         5.92 
TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       13.94        33.27         0.85        20.12        18.64         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A93C 
        0.79        23.41        14.50        44.75         3.68        23.18 
TCGA-L5-A43H TCGA-L5-A4OT TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G 
        0.30         4.90        13.48        13.55        83.24        10.85 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 
       13.41        13.15        12.59        13.25        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HZ 
       11.54        13.22         4.47        25.25        10.52        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-V5-A7RC 
       12.33        13.38         0.13        12.85        12.26         3.42 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 
        8.12        28.11        18.18        18.05        11.24        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.66 

$`DEL PEAK 25(10P11.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF 
       22.82         0.36        35.97         5.16        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
       32.45         7.69        35.21        20.78         2.63         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30        17.03        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16       122.10        68.02        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.02        55.50         2.66        12.92        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       12.33        13.38        15.35        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 
       12.76        12.59        12.85        15.52        12.33        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       12.43         1.55        18.31        33.70        52.27        46.19 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        9.17        15.91        18.21         2.10         1.32        19.73 

  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                           0.13                            0.36 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                         13.200                          12.835 
[1] "0.1 - 83.2 (13.2)"  "0.4 - 122.1 (12.8)"
[1] "hr=" "1.4"
D55V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(10P11.21) MUTATED         1        0        1        0        20
  DEL PEAK 25(10P11.21) WILD-TYPE       7        5        5        1        27
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10P11.21) MUTATED          10         6          4          3
  DEL PEAK 25(10P11.21) WILD-TYPE        21        19         10          6
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(10P11.21) MUTATED            1        3         1
  DEL PEAK 25(10P11.21) WILD-TYPE          6        2         3
D55V3, multiclass
            clus
vv           DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               0                               5
  STAGE IB                               1                               5
  STAGE II                               0                               1
  STAGE IIA                             20                              27
  STAGE IIB                             10                              21
  STAGE III                              6                              19
  STAGE IIIA                             4                              10
  STAGE IIIB                             3                               6
  STAGE IIIC                             1                               6
  STAGE IV                               3                               2
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 25(10P11.21) MUTATED       4 16 29  1
  DEL PEAK 25(10P11.21) WILD-TYPE    28 27 58  4
D55V4, multiclass
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  T0+T1                             4                              28
  T2                               16                              27
  T3                               29                              58
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 25(10P11.21) MUTATED   26 17  4  2
  DEL PEAK 25(10P11.21) WILD-TYPE 51 51  8  6
D55V5, multiclass
    clus
vv   DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  N0                            26                              51
  N1                            17                              51
  N2                             4                               8
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED   44  4
  DEL PEAK 25(10P11.21) WILD-TYPE 91  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED     44    4
  DEL PEAK 25(10P11.21) WILD-TYPE   91    5
   clus
vv  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  0                            44                              91
  1                             4                               5
[1] 2 2
[1] FALSE
D55V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10P11.21) MUTATED     7  45
  DEL PEAK 25(10P11.21) WILD-TYPE  20 112
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      7   45
  DEL PEAK 25(10P11.21) WILD-TYPE   20  112
        clus
vv       DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  FEMALE                             7                              20
  MALE                              45                             112
[1] 2 2
[1] FALSE
D55V8, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED   35 12
  DEL PEAK 25(10P11.21) WILD-TYPE 88 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED     35   12
  DEL PEAK 25(10P11.21) WILD-TYPE   88   31
     clus
vv    DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  NO                             35                              88
  YES                            12                              31
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED   10 42
  DEL PEAK 25(10P11.21) WILD-TYPE 78 54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED     10   42
  DEL PEAK 25(10P11.21) WILD-TYPE   78   54
                                   clus
vv                                  DEL PEAK 25(10P11.21) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                10
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            42
                                   clus
vv                                  DEL PEAK 25(10P11.21) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              54
[1] 2 2
[1] FALSE
D55V11, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(10P11.21) MUTATED    37   6   1   2
  DEL PEAK 25(10P11.21) WILD-TYPE 100   6   1   5
D55V12, multiclass
    clus
vv   DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  R0                            37                             100
  R1                             6                               6
  R2                             1                               1
  RX                             2                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10P11.21) MUTATED      22                         4    22
  DEL PEAK 25(10P11.21) WILD-TYPE    24                         1    92
D55V14, multiclass
                           clus
vv                          DEL PEAK 25(10P11.21) MUTATED
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                22
                           clus
vv                          DEL PEAK 25(10P11.21) WILD-TYPE
  ASIAN                                                  24
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED    3 28
  DEL PEAK 25(10P11.21) WILD-TYPE  3 60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      3   28
  DEL PEAK 25(10P11.21) WILD-TYPE    3   60
                        clus
vv                       DEL PEAK 25(10P11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            28
                        clus
vv                       DEL PEAK 25(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              60
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 26(10Q21.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(10Q21.1) MUTATED   31 15
  DEL PEAK 26(10Q21.1) WILD-TYPE 77 61
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            46                            138 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            15                             61 
$`DEL PEAK 26(10Q21.1) MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IG-A3I8 
       24.00         4.70        27.12        14.30        13.94        33.27 
TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A93C 
        0.85         0.53        23.41        14.50        68.02        23.18 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
        3.16         0.30        21.01         1.38         3.16         4.90 
TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 
       13.55        83.24        10.85        13.38        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        22.39        12.85        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       25.25        12.00        12.03        13.18        13.38        13.18 
TCGA-LN-A9FR TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EX 
       12.26        53.95        15.78         3.42        16.44        28.11 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        14.37         2.10         1.32 

$`DEL PEAK 26(10Q21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        35.97         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        0.79        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF 
       31.56        25.22        24.03         6.28        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       32.61        47.93        18.35         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35        12.59        13.25        12.62        12.76        12.59 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A8HZ 
       15.52        11.54         4.47        10.52        12.23        12.33 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        5.29        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        18.21        41.23         3.42         2.66        19.73 

  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                        13.200                         12.835 
[1] "0.3 - 83.2 (13.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.3"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10Q21.1) MUTATED         2        1        1        1        15
  DEL PEAK 26(10Q21.1) WILD-TYPE       6        4        5        0        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q21.1) MUTATED           7         5          5          2
  DEL PEAK 26(10Q21.1) WILD-TYPE        24        20          9          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(10Q21.1) MUTATED            0        1         2
  DEL PEAK 26(10Q21.1) WILD-TYPE          7        4         2
D56V3, multiclass
            clus
vv           DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  STAGE I                               2                              6
  STAGE IA                              1                              4
  STAGE IB                              1                              5
  STAGE II                              1                              0
  STAGE IIA                            15                             32
  STAGE IIB                             7                             24
  STAGE III                             5                             20
  STAGE IIIA                            5                              9
  STAGE IIIB                            2                              7
  STAGE IIIC                            0                              7
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 26(10Q21.1) MUTATED       7 13 21  1
  DEL PEAK 26(10Q21.1) WILD-TYPE    25 30 66  4
D56V4, multiclass
       clus
vv      DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  T0+T1                            7                             25
  T2                              13                             30
  T3                              21                             66
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 26(10Q21.1) MUTATED   22 16  3  0
  DEL PEAK 26(10Q21.1) WILD-TYPE 55 52  9  8
D56V5, multiclass
    clus
vv   DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  N0                           22                             55
  N1                           16                             52
  N2                            3                              9
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED   36  3
  DEL PEAK 26(10Q21.1) WILD-TYPE 99  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED     36    3
  DEL PEAK 26(10Q21.1) WILD-TYPE   99    6
   clus
vv  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  0                           36                             99
  1                            3                              6
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q21.1) MUTATED     7  39
  DEL PEAK 26(10Q21.1) WILD-TYPE  20 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED      7   39
  DEL PEAK 26(10Q21.1) WILD-TYPE   20  118
        clus
vv       DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  FEMALE                            7                             20
  MALE                             39                            118
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED   32 10
  DEL PEAK 26(10Q21.1) WILD-TYPE 91 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED     32   10
  DEL PEAK 26(10Q21.1) WILD-TYPE   91   33
     clus
vv    DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  NO                            32                             91
  YES                           10                             33
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED   15 31
  DEL PEAK 26(10Q21.1) WILD-TYPE 73 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED     15   31
  DEL PEAK 26(10Q21.1) WILD-TYPE   73   65
                                   clus
vv                                  DEL PEAK 26(10Q21.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               15
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           31
                                   clus
vv                                  DEL PEAK 26(10Q21.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 73
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             65
[1] 2 2
[1] FALSE
D56V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10Q21.1) MUTATED    33   5   0   2
  DEL PEAK 26(10Q21.1) WILD-TYPE 104   7   2   5
D56V12, multiclass
    clus
vv   DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  R0                           33                            104
  R1                            5                              7
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10Q21.1) MUTATED      20                         4    19
  DEL PEAK 26(10Q21.1) WILD-TYPE    26                         1    95
D56V14, multiclass
                           clus
vv                          DEL PEAK 26(10Q21.1) MUTATED
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               19
                           clus
vv                          DEL PEAK 26(10Q21.1) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED    2 28
  DEL PEAK 26(10Q21.1) WILD-TYPE  4 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED      2   28
  DEL PEAK 26(10Q21.1) WILD-TYPE    4   60
                        clus
vv                       DEL PEAK 26(10Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 26(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             60
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 27(10Q23.31) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 27(10Q23.31) MUTATED   39 26
  DEL PEAK 27(10Q23.31) WILD-TYPE 69 50
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             65                             119 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             26                              50 
$`DEL PEAK 27(10Q23.31) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.31         8.94        24.00         4.70        27.12         5.16 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
       33.27        35.21         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH 
       14.50        44.75        23.18         3.16         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
       21.01         3.32         3.16        58.59         4.90         7.13 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49L 
       55.50        13.48        13.55        83.24        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 
       12.66        13.38        12.46        12.59        12.49        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.85        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6DQ 
       12.00        12.03        13.38        13.18        12.26         7.59 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP 
        5.06        53.95         2.89         3.42        16.44        27.09 
TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       28.11        25.08        14.37         2.10         1.32 

$`DEL PEAK 27(10Q23.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.36        35.97        20.02        31.27        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        8.94        32.45         7.69        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        6.28        30.25        26.33        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        1.38        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.40         3.75         3.02         2.66        12.92        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.36         5.92        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HX 
       12.76        12.59        15.52        11.54         4.47        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       13.18        12.33         0.13        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        5.29        15.35         9.27         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        41.23         3.42         2.66        19.73 

  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                           0.30                            0.13 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                          12.66                           13.18 
[1] "0.3 - 83.2 (12.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D57V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q23.31) MUTATED         3        1        1        1        17
  DEL PEAK 27(10Q23.31) WILD-TYPE       5        4        5        0        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q23.31) MUTATED          12         9          5          4
  DEL PEAK 27(10Q23.31) WILD-TYPE        19        16          9          5
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(10Q23.31) MUTATED            1        1         2
  DEL PEAK 27(10Q23.31) WILD-TYPE          6        4         2
D57V3, multiclass
            clus
vv           DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               4
  STAGE IB                               1                               5
  STAGE II                               1                               0
  STAGE IIA                             17                              30
  STAGE IIB                             12                              19
  STAGE III                              9                              16
  STAGE IIIA                             5                               9
  STAGE IIIB                             4                               5
  STAGE IIIC                             1                               6
  STAGE IV                               1                               4
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 27(10Q23.31) MUTATED       8 19 30  1
  DEL PEAK 27(10Q23.31) WILD-TYPE    24 24 57  4
D57V4, multiclass
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  T0+T1                             8                              24
  T2                               19                              24
  T3                               30                              57
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 27(10Q23.31) MUTATED   26 25  5  1
  DEL PEAK 27(10Q23.31) WILD-TYPE 51 43  7  7
D57V5, multiclass
    clus
vv   DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  N0                            26                              51
  N1                            25                              43
  N2                             5                               7
  N3                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   51  3
  DEL PEAK 27(10Q23.31) WILD-TYPE 84  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     51    3
  DEL PEAK 27(10Q23.31) WILD-TYPE   84    6
   clus
vv  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  0                            51                              84
  1                             3                               6
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10Q23.31) MUTATED    11  54
  DEL PEAK 27(10Q23.31) WILD-TYPE  16 103
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     11   54
  DEL PEAK 27(10Q23.31) WILD-TYPE   16  103
        clus
vv       DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  FEMALE                            11                              16
  MALE                              54                             103
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   44 14
  DEL PEAK 27(10Q23.31) WILD-TYPE 79 29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     44   14
  DEL PEAK 27(10Q23.31) WILD-TYPE   79   29
     clus
vv    DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  NO                             44                              79
  YES                            14                              29
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   27 38
  DEL PEAK 27(10Q23.31) WILD-TYPE 61 58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     27   38
  DEL PEAK 27(10Q23.31) WILD-TYPE   61   58
                                   clus
vv                                  DEL PEAK 27(10Q23.31) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                27
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            38
                                   clus
vv                                  DEL PEAK 27(10Q23.31) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              58
[1] 2 2
[1] FALSE
D57V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 27(10Q23.31) MUTATED   44  8  0  5
  DEL PEAK 27(10Q23.31) WILD-TYPE 93  4  2  2
D57V12, multiclass
    clus
vv   DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  R0                            44                              93
  R1                             8                               4
  R2                             0                               2
  RX                             5                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10Q23.31) MUTATED      22                         4    30
  DEL PEAK 27(10Q23.31) WILD-TYPE    24                         1    84
D57V14, multiclass
                           clus
vv                          DEL PEAK 27(10Q23.31) MUTATED
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                30
                           clus
vv                          DEL PEAK 27(10Q23.31) WILD-TYPE
  ASIAN                                                  24
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED    2 35
  DEL PEAK 27(10Q23.31) WILD-TYPE  4 53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED      2   35
  DEL PEAK 27(10Q23.31) WILD-TYPE    4   53
                        clus
vv                       DEL PEAK 27(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            35
                        clus
vv                       DEL PEAK 27(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              53
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 28(11P15.4) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(11P15.4) MUTATED   55 24
  DEL PEAK 28(11P15.4) WILD-TYPE 53 52
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            79                            105 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            24                             52 
$`DEL PEAK 28(11P15.4) MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-S8-A6BV 
       34.85         4.31         8.94         4.70         0.36        20.02 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        14.30         5.92         4.21        32.45         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H 
        0.85         2.63         0.53        25.22         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       26.33        32.61         3.32         7.17         1.38         3.16 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NJ 
       15.48         2.60         3.75         3.02        55.50        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.55        13.22        13.41        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.62        12.59        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        12.03        13.18         0.13        12.85        12.26 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
       38.40        53.95        15.78         2.30        12.69         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW 
       16.44         9.27         8.98        27.09        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 
       28.11        18.18        11.24        15.91        25.08        14.37 
TCGA-Z6-A8JE 
        2.10 

$`DEL PEAK 28(11P15.4) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        18.28        24.00        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
       35.97        27.12         5.16        25.78        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       13.94         8.94        16.24        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS TCGA-L5-A4OT 
       30.25        21.01        47.93        18.35        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF 
       29.00         7.13         7.43        25.12         7.40         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       83.24        52.57        46.09        12.59        13.25        12.46 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.59        22.39        15.52        11.54        10.52        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        12.33        13.38        12.03        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         2.89         7.00        20.38         5.29        15.35 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 
       25.81        22.82         1.55        18.31        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD 
       46.19        18.05         9.17        18.21        41.23         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                          0.13                           0.79 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                          55.5                          122.1 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                         12.43                          15.52 
[1] "0.1 - 55.5 (12.4)"  "0.8 - 122.1 (15.5)"
[1] "hr=" "1"  
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(11P15.4) MUTATED         3        2        2        1        18
  DEL PEAK 28(11P15.4) WILD-TYPE       5        3        4        0        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(11P15.4) MUTATED          12        13          7          2
  DEL PEAK 28(11P15.4) WILD-TYPE        19        12          7          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(11P15.4) MUTATED            3        2         2
  DEL PEAK 28(11P15.4) WILD-TYPE          4        3         2
D58V3, multiclass
            clus
vv           DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              2                              3
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            18                             29
  STAGE IIB                            12                             19
  STAGE III                            13                             12
  STAGE IIIA                            7                              7
  STAGE IIIB                            2                              7
  STAGE IIIC                            3                              4
  STAGE IV                              2                              3
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 28(11P15.4) MUTATED      12 14 41  3
  DEL PEAK 28(11P15.4) WILD-TYPE    20 29 46  2
D58V4, multiclass
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  T0+T1                           12                             20
  T2                              14                             29
  T3                              41                             46
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 28(11P15.4) MUTATED   32 30  4  4
  DEL PEAK 28(11P15.4) WILD-TYPE 45 38  8  4
D58V5, multiclass
    clus
vv   DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  N0                           32                             45
  N1                           30                             38
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED   55  4
  DEL PEAK 28(11P15.4) WILD-TYPE 80  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED     55    4
  DEL PEAK 28(11P15.4) WILD-TYPE   80    5
   clus
vv  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  0                           55                             80
  1                            4                              5
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    7 72
  DEL PEAK 28(11P15.4) WILD-TYPE 20 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      7   72
  DEL PEAK 28(11P15.4) WILD-TYPE   20   85
        clus
vv       DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  FEMALE                            7                             20
  MALE                             72                             85
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED   47 22
  DEL PEAK 28(11P15.4) WILD-TYPE 76 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED     47   22
  DEL PEAK 28(11P15.4) WILD-TYPE   76   21
     clus
vv    DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  NO                            47                             76
  YES                           22                             21
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED   35 44
  DEL PEAK 28(11P15.4) WILD-TYPE 53 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED     35   44
  DEL PEAK 28(11P15.4) WILD-TYPE   53   52
                                   clus
vv                                  DEL PEAK 28(11P15.4) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               35
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           44
                                   clus
vv                                  DEL PEAK 28(11P15.4) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 53
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             52
[1] 2 2
[1] FALSE
D58V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 28(11P15.4) MUTATED   57  5  2  3
  DEL PEAK 28(11P15.4) WILD-TYPE 80  7  0  4
D58V12, multiclass
    clus
vv   DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  R0                           57                             80
  R1                            5                              7
  R2                            2                              0
  RX                            3                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11P15.4) MUTATED      27                         4    40
  DEL PEAK 28(11P15.4) WILD-TYPE    19                         1    74
D58V14, multiclass
                           clus
vv                          DEL PEAK 28(11P15.4) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               40
                           clus
vv                          DEL PEAK 28(11P15.4) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    3 41
  DEL PEAK 28(11P15.4) WILD-TYPE  3 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      3   41
  DEL PEAK 28(11P15.4) WILD-TYPE    3   47
                        clus
vv                       DEL PEAK 28(11P15.4) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK 28(11P15.4) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             47
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 29(11Q25) MUTATION ANALYSIS
D59V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 29(11Q25) MUTATED   48 33
  DEL PEAK 29(11Q25) WILD-TYPE 60 43
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          81                          103 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          33                           43 
$`DEL PEAK 29(11Q25) MUTATED`
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       27.12         5.16        20.02        14.30         7.63         5.92 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         3.88        17.03        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       14.50        12.16        47.38         3.16         0.30        26.33 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S 
       47.93         3.32         7.17         3.16        29.00        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.55        13.22        52.57        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W 
       10.45        12.66        12.43        13.38        12.59        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22        12.33        25.25        12.00        12.23 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        12.03        12.85         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.59         5.06         6.35         2.89         2.30        12.69 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        3.42        25.81        12.43        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.18        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       14.37         2.10         1.32 

$`DEL PEAK 29(11Q25) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
       20.78         2.63         9.30         0.53         0.79        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        6.28        30.25        32.61        21.01        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
       58.59         4.90         7.13         7.43        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       13.41        83.24        46.09        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 
       15.35        12.62        12.46        12.59        11.54         4.47 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FR 
       10.52        12.03        13.18        12.33        13.38        12.26 
TCGA-M9-A5M8 TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       33.11        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EY 
        9.27         8.98        27.09        22.82         1.55        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       52.27        46.19        18.05        18.21         3.42         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        0.13                         0.36 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        55.5                        122.1 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                       12.49                        15.35 
[1] "0.1 - 55.5 (12.5)"  "0.4 - 122.1 (15.3)"
[1] "hr=" "1.4"
D59V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11Q25) MUTATED         1        3        1        1        23
  DEL PEAK 29(11Q25) WILD-TYPE       7        2        5        0        24
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11Q25) MUTATED          12        12          4          4
  DEL PEAK 29(11Q25) WILD-TYPE        19        13         10          5
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(11Q25) MUTATED            4        3         2
  DEL PEAK 29(11Q25) WILD-TYPE          3        2         2
D59V3, multiclass
            clus
vv           DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            3                            2
  STAGE IB                            1                            5
  STAGE II                            1                            0
  STAGE IIA                          23                           24
  STAGE IIB                          12                           19
  STAGE III                          12                           13
  STAGE IIIA                          4                           10
  STAGE IIIB                          4                            5
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 29(11Q25) MUTATED      11 21 37  2
  DEL PEAK 29(11Q25) WILD-TYPE    21 22 50  3
D59V4, multiclass
       clus
vv      DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  T0+T1                         11                           21
  T2                            21                           22
  T3                            37                           50
  T4                             2                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 29(11Q25) MUTATED   33 28  4  5
  DEL PEAK 29(11Q25) WILD-TYPE 44 40  8  3
D59V5, multiclass
    clus
vv   DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  N0                         33                           44
  N1                         28                           40
  N2                          4                            8
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED   58  5
  DEL PEAK 29(11Q25) WILD-TYPE 77  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED     58    5
  DEL PEAK 29(11Q25) WILD-TYPE   77    4
   clus
vv  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  0                         58                           77
  1                          5                            4
[1] 2 2
[1] FALSE
D59V7, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED   11 70
  DEL PEAK 29(11Q25) WILD-TYPE 16 87
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED     11   70
  DEL PEAK 29(11Q25) WILD-TYPE   16   87
        clus
vv       DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  FEMALE                         11                           16
  MALE                           70                           87
[1] 2 2
[1] FALSE
D59V8, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED   49 22
  DEL PEAK 29(11Q25) WILD-TYPE 74 21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED     49   22
  DEL PEAK 29(11Q25) WILD-TYPE   74   21
     clus
vv    DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  NO                          49                           74
  YES                         22                           21
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED   30 51
  DEL PEAK 29(11Q25) WILD-TYPE 58 45
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED     30   51
  DEL PEAK 29(11Q25) WILD-TYPE   58   45
                                   clus
vv                                  DEL PEAK 29(11Q25) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         51
                                   clus
vv                                  DEL PEAK 29(11Q25) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           45
[1] 2 2
[1] FALSE
D59V11, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 29(11Q25) MUTATED   57  5  1  4
  DEL PEAK 29(11Q25) WILD-TYPE 80  7  1  3
D59V12, multiclass
    clus
vv   DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  R0                         57                           80
  R1                          5                            7
  R2                          1                            1
  RX                          4                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11Q25) MUTATED      25                         4    46
  DEL PEAK 29(11Q25) WILD-TYPE    21                         1    68
D59V14, multiclass
                           clus
vv                          DEL PEAK 29(11Q25) MUTATED
  ASIAN                                             25
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             46
                           clus
vv                          DEL PEAK 29(11Q25) WILD-TYPE
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            1
  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"
D59V15, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED    4 44
  DEL PEAK 29(11Q25) WILD-TYPE  2 44
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED      4   44
  DEL PEAK 29(11Q25) WILD-TYPE    2   44
                        clus
vv                       DEL PEAK 29(11Q25) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         44
                        clus
vv                       DEL PEAK 29(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 30(12Q23.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(12Q23.1) MUTATED   34 18
  DEL PEAK 30(12Q23.1) WILD-TYPE 74 58
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            52                            132 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            18                             58 
$`DEL PEAK 30(12Q23.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-2H-A9GF 
       34.85        18.28         8.94         0.36        20.02        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB 
       31.27        14.30        13.94        32.45        33.27         2.63 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FH 
       18.64         0.79        23.41        14.50        68.02        47.38 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
       25.22        30.25        32.61        21.01         3.32         7.17 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       58.59         7.13         2.60         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NS TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49O 
       12.92        13.48        13.41        10.85        12.66        13.41 
TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A8W8 
       12.59        12.33        12.85         7.82         5.06         2.89 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA7B 
       20.38         3.42         8.98         1.55        52.27        11.24 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       18.21        25.08        14.37         2.66 

$`DEL PEAK 30(12Q23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GJ TCGA-2H-A9GK 
       22.82        35.97        27.12         5.16        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
        5.92         8.94        16.24         4.21         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        0.85        20.78        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
      122.10        44.75         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93        18.35         1.38         3.16         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ 
        7.43        15.48        25.12         7.40         3.75        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00         5.29        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       28.11        33.70        18.18        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       15.91        41.23         3.42         2.10         1.32        19.73 

  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                          0.36                           0.13 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                         68.02                         122.10 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                        13.445                         12.790 
[1] "0.4 - 68.0 (13.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(12Q23.1) MUTATED         4        1        2        0        10
  DEL PEAK 30(12Q23.1) WILD-TYPE       4        4        4        1        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(12Q23.1) MUTATED          13         4          5          1
  DEL PEAK 30(12Q23.1) WILD-TYPE        18        21          9          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(12Q23.1) MUTATED            1        2         1
  DEL PEAK 30(12Q23.1) WILD-TYPE          6        3         3
D60V3, multiclass
            clus
vv           DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            10                             37
  STAGE IIB                            13                             18
  STAGE III                             4                             21
  STAGE IIIA                            5                              9
  STAGE IIIB                            1                              8
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(12Q23.1) MUTATED      12 10 25  0
  DEL PEAK 30(12Q23.1) WILD-TYPE    20 33 62  5
D60V4, multiclass
       clus
vv      DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  T0+T1                           12                             20
  T2                              10                             33
  T3                              25                             62
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 30(12Q23.1) MUTATED   22 20  2  2
  DEL PEAK 30(12Q23.1) WILD-TYPE 55 48 10  6
D60V5, multiclass
    clus
vv   DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  N0                           22                             55
  N1                           20                             48
  N2                            2                             10
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED   36  3
  DEL PEAK 30(12Q23.1) WILD-TYPE 99  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     36    3
  DEL PEAK 30(12Q23.1) WILD-TYPE   99    6
   clus
vv  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  0                           36                             99
  1                            3                              6
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(12Q23.1) MUTATED    10  42
  DEL PEAK 30(12Q23.1) WILD-TYPE  17 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     10   42
  DEL PEAK 30(12Q23.1) WILD-TYPE   17  115
        clus
vv       DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  FEMALE                           10                             17
  MALE                             42                            115
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED   36 10
  DEL PEAK 30(12Q23.1) WILD-TYPE 87 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     36   10
  DEL PEAK 30(12Q23.1) WILD-TYPE   87   33
     clus
vv    DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  NO                            36                             87
  YES                           10                             33
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED   31 21
  DEL PEAK 30(12Q23.1) WILD-TYPE 57 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     31   21
  DEL PEAK 30(12Q23.1) WILD-TYPE   57   75
                                   clus
vv                                  DEL PEAK 30(12Q23.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           21
                                   clus
vv                                  DEL PEAK 30(12Q23.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 57
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             75
[1] 2 2
[1] FALSE
D60V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 30(12Q23.1) MUTATED   38  4  0  2
  DEL PEAK 30(12Q23.1) WILD-TYPE 99  8  2  5
D60V12, multiclass
    clus
vv   DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  R0                           38                             99
  R1                            4                              8
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q23.1) MUTATED       7                         4    34
  DEL PEAK 30(12Q23.1) WILD-TYPE    39                         1    80
D60V14, multiclass
                           clus
vv                          DEL PEAK 30(12Q23.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               34
                           clus
vv                          DEL PEAK 30(12Q23.1) WILD-TYPE
  ASIAN                                                 39
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED    2 21
  DEL PEAK 30(12Q23.1) WILD-TYPE  4 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED      2   21
  DEL PEAK 30(12Q23.1) WILD-TYPE    4   67
                        clus
vv                       DEL PEAK 30(12Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK 30(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             67
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 31(13Q12.11) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 31(13Q12.11) MUTATED   46 30
  DEL PEAK 31(13Q12.11) WILD-TYPE 62 46
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             76                             108 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             30                              46 
$`DEL PEAK 31(13Q12.11) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
       60.39         8.94         5.16        25.78        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        8.94        32.45        35.21         0.85        20.78         2.63 
TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        3.88        17.03         0.79        23.41         9.96         4.67 
TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR 
       68.02        23.18        25.22        26.33        47.93         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU 
        4.90        29.00        15.48        13.22         5.49        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        13.38        13.15        15.35        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        12.85        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.33        10.52        12.23        12.03        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WC 
        0.13        12.26         5.06        38.40         6.35         2.30 
TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       12.69        16.44        15.35        25.81        27.09        22.82 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
       18.31        28.11        33.70        18.18        52.27        11.24 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        41.23        14.37         2.10 

$`DEL PEAK 31(13Q12.11) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV 
       19.99        22.82         0.36        35.97        27.12        20.02 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
        7.69        33.27        20.12        18.64         9.30         0.53 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        47.38        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
       18.35         3.32         7.17         1.38        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49P 
        7.76        21.37         8.71        13.41        52.57        12.33 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.59        12.62        12.46        12.59        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I1 
       13.22         4.47        25.25        12.00        13.18        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31         7.04        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.38         5.29         3.42         9.27         8.98 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43         1.55         8.12        46.19        18.05         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        25.08         3.42         1.32         2.66        19.73 

  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                           0.13                            0.30 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                         13.185                          12.885 
[1] "0.1 - 83.2 (13.2)"  "0.3 - 122.1 (12.9)"
[1] "hr=" "1.2"
D61V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(13Q12.11) MUTATED         2        2        4        1        22
  DEL PEAK 31(13Q12.11) WILD-TYPE       6        3        2        0        25
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(13Q12.11) MUTATED           9        12          6          5
  DEL PEAK 31(13Q12.11) WILD-TYPE        22        13          8          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(13Q12.11) MUTATED            2        3         1
  DEL PEAK 31(13Q12.11) WILD-TYPE          5        2         3
D61V3, multiclass
            clus
vv           DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  STAGE I                                2                               6
  STAGE IA                               2                               3
  STAGE IB                               4                               2
  STAGE II                               1                               0
  STAGE IIA                             22                              25
  STAGE IIB                              9                              22
  STAGE III                             12                              13
  STAGE IIIA                             6                               8
  STAGE IIIB                             5                               4
  STAGE IIIC                             2                               5
  STAGE IV                               3                               2
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 31(13Q12.11) MUTATED      10 18 39  3
  DEL PEAK 31(13Q12.11) WILD-TYPE    22 25 48  2
D61V4, multiclass
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  T0+T1                            10                              22
  T2                               18                              25
  T3                               39                              48
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 31(13Q12.11) MUTATED   35 26  6  3
  DEL PEAK 31(13Q12.11) WILD-TYPE 42 42  6  5
D61V5, multiclass
    clus
vv   DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  N0                            35                              42
  N1                            26                              42
  N2                             6                               6
  N3                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED   59  4
  DEL PEAK 31(13Q12.11) WILD-TYPE 76  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED     59    4
  DEL PEAK 31(13Q12.11) WILD-TYPE   76    5
   clus
vv  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  0                            59                              76
  1                             4                               5
[1] 2 2
[1] FALSE
D61V7, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    8 68
  DEL PEAK 31(13Q12.11) WILD-TYPE 19 89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      8   68
  DEL PEAK 31(13Q12.11) WILD-TYPE   19   89
        clus
vv       DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  FEMALE                             8                              19
  MALE                              68                              89
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED   48 24
  DEL PEAK 31(13Q12.11) WILD-TYPE 75 19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED     48   24
  DEL PEAK 31(13Q12.11) WILD-TYPE   75   19
     clus
vv    DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  NO                             48                              75
  YES                            24                              19
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED   26 50
  DEL PEAK 31(13Q12.11) WILD-TYPE 62 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED     26   50
  DEL PEAK 31(13Q12.11) WILD-TYPE   62   46
                                   clus
vv                                  DEL PEAK 31(13Q12.11) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                26
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            50
                                   clus
vv                                  DEL PEAK 31(13Q12.11) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              46
[1] 2 2
[1] FALSE
D61V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 31(13Q12.11) MUTATED   58  3  1  4
  DEL PEAK 31(13Q12.11) WILD-TYPE 79  9  1  3
D61V12, multiclass
    clus
vv   DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  R0                            58                              79
  R1                             3                               9
  R2                             1                               1
  RX                             4                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(13Q12.11) MUTATED      26                         3    40
  DEL PEAK 31(13Q12.11) WILD-TYPE    20                         2    74
D61V14, multiclass
                           clus
vv                          DEL PEAK 31(13Q12.11) MUTATED
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                40
                           clus
vv                          DEL PEAK 31(13Q12.11) WILD-TYPE
  ASIAN                                                  20
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    3 42
  DEL PEAK 31(13Q12.11) WILD-TYPE  3 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      3   42
  DEL PEAK 31(13Q12.11) WILD-TYPE    3   46
                        clus
vv                       DEL PEAK 31(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            42
                        clus
vv                       DEL PEAK 31(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              46
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(13Q14.2) MUTATED   45 29
  DEL PEAK 32(13Q14.2) WILD-TYPE 63 47
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            74                            110 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            29                             47 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN 
       60.39        24.00        25.78        58.55         7.63         8.94 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       35.21         0.85        20.78         2.63         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       17.03        23.41         9.96        44.75        68.02         3.68 
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       25.22        26.33        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU 
        3.75         3.02        13.48        13.22         5.49        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.25        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       11.54        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6KZ 
       12.33        13.38        13.18         0.13        12.26         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP 
       38.40         6.35        12.69        16.44        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA7I TCGA-XP-A8T8 
       15.91        14.37 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       20.02        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
        4.21        32.45         7.69        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       12.16       122.10        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40        55.50         2.66        12.92        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49P 
        7.76        21.37         8.71        13.41        52.57        12.33 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.62        12.46        12.59        15.52        12.33         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       25.25        12.00        13.18        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        7.82         8.02         7.59        16.31         7.04        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        5.29         3.42        15.35         9.27         8.98        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55         8.12        46.19        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                          0.13                           0.30 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                         13.22                          12.72 
[1] "0.1 - 83.2 (13.2)"  "0.3 - 122.1 (12.7)"
[1] "hr=" "1.3"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(13Q14.2) MUTATED         4        2        2        1        23
  DEL PEAK 32(13Q14.2) WILD-TYPE       4        3        4        0        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(13Q14.2) MUTATED           9        14          6          3
  DEL PEAK 32(13Q14.2) WILD-TYPE        22        11          8          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(13Q14.2) MUTATED            2        1         1
  DEL PEAK 32(13Q14.2) WILD-TYPE          5        4         3
D62V3, multiclass
            clus
vv           DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            23                             24
  STAGE IIB                             9                             22
  STAGE III                            14                             11
  STAGE IIIA                            6                              8
  STAGE IIIB                            3                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              4
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 32(13Q14.2) MUTATED      12 20 34  3
  DEL PEAK 32(13Q14.2) WILD-TYPE    20 23 53  2
D62V4, multiclass
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  T0+T1                           12                             20
  T2                              20                             23
  T3                              34                             53
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 32(13Q14.2) MUTATED   35 29  3  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 42 39  9  6
D62V5, multiclass
    clus
vv   DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  N0                           35                             42
  N1                           29                             39
  N2                            3                              9
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED   62  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 73  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     62    2
  DEL PEAK 32(13Q14.2) WILD-TYPE   73    7
   clus
vv  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  0                           62                             73
  1                            2                              7
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    7 67
  DEL PEAK 32(13Q14.2) WILD-TYPE 20 90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      7   67
  DEL PEAK 32(13Q14.2) WILD-TYPE   20   90
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                            7                             20
  MALE                             67                             90
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED   45 25
  DEL PEAK 32(13Q14.2) WILD-TYPE 78 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     45   25
  DEL PEAK 32(13Q14.2) WILD-TYPE   78   18
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  NO                            45                             78
  YES                           25                             18
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED   26 48
  DEL PEAK 32(13Q14.2) WILD-TYPE 62 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     26   48
  DEL PEAK 32(13Q14.2) WILD-TYPE   62   48
                                   clus
vv                                  DEL PEAK 32(13Q14.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               26
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           48
                                   clus
vv                                  DEL PEAK 32(13Q14.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             48
[1] 2 2
[1] FALSE
D62V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 32(13Q14.2) MUTATED   61  1  1  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 76 11  1  5
D62V12, multiclass
    clus
vv   DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  R0                           61                             76
  R1                            1                             11
  R2                            1                              1
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED      29                         2    38
  DEL PEAK 32(13Q14.2) WILD-TYPE    17                         3    76
D62V14, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               38
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    2 40
  DEL PEAK 32(13Q14.2) WILD-TYPE  4 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      2   40
  DEL PEAK 32(13Q14.2) WILD-TYPE    4   48
                        clus
vv                       DEL PEAK 32(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 32(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             48
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 33(13Q21.31) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 33(13Q21.31) MUTATED   40 29
  DEL PEAK 33(13Q21.31) WILD-TYPE 68 47
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             69                             115 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             29                              47 
$`DEL PEAK 33(13Q21.31) MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR 
       60.39        24.00        58.55         7.63         8.94        32.45 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       35.21         0.85        20.78         2.63         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A93E 
       17.03        23.41         9.96        44.75        68.02        25.22 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V 
       26.33        21.01        47.93         3.16        29.00         2.60 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       13.48        13.22         5.49        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        10.45        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        13.25        12.46        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       22.39        12.85        13.22        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR 
       12.03        12.33        13.38        13.18         0.13        12.26 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE 
        7.59         5.06         6.35         9.30        12.69        16.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ 
       25.81        27.09        22.82        18.31        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T8 
       52.27        15.91        14.37 

$`DEL PEAK 33(13Q21.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM 
       20.02        25.78        31.27        14.30         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         4.21         7.69        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16       122.10         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        0.30        32.61        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
       58.59         4.90         7.13         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         7.76        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 
       52.57        12.66        12.33        12.59        12.62        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        15.52        11.54        12.33         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.00        13.18        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        8.02        16.31         7.04        38.40        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       15.35         9.27         8.98        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       33.70        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                           0.13                            0.30 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                          13.22                           12.66 
[1] "0.1 - 83.2 (13.2)"  "0.3 - 122.1 (12.7)"
[1] "hr=" "1.1"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q21.31) MUTATED         3        2        2        1        21
  DEL PEAK 33(13Q21.31) WILD-TYPE       5        3        4        0        26
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q21.31) MUTATED           9        12          6          3
  DEL PEAK 33(13Q21.31) WILD-TYPE        22        13          8          6
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(13Q21.31) MUTATED            2        1         1
  DEL PEAK 33(13Q21.31) WILD-TYPE          5        4         3
D63V3, multiclass
            clus
vv           DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               2                               3
  STAGE IB                               2                               4
  STAGE II                               1                               0
  STAGE IIA                             21                              26
  STAGE IIB                              9                              22
  STAGE III                             12                              13
  STAGE IIIA                             6                               8
  STAGE IIIB                             3                               6
  STAGE IIIC                             2                               5
  STAGE IV                               1                               4
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 33(13Q21.31) MUTATED      11 18 31  3
  DEL PEAK 33(13Q21.31) WILD-TYPE    21 25 56  2
D63V4, multiclass
       clus
vv      DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  T0+T1                            11                              21
  T2                               18                              25
  T3                               31                              56
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 33(13Q21.31) MUTATED   32 26  3  2
  DEL PEAK 33(13Q21.31) WILD-TYPE 45 42  9  6
D63V5, multiclass
    clus
vv   DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  N0                            32                              45
  N1                            26                              42
  N2                             3                               9
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED   55  2
  DEL PEAK 33(13Q21.31) WILD-TYPE 80  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED     55    2
  DEL PEAK 33(13Q21.31) WILD-TYPE   80    7
   clus
vv  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  0                            55                              80
  1                             2                               7
[1] 2 2
[1] FALSE
D63V7, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED    6 63
  DEL PEAK 33(13Q21.31) WILD-TYPE 21 94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED      6   63
  DEL PEAK 33(13Q21.31) WILD-TYPE   21   94
        clus
vv       DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  FEMALE                             6                              21
  MALE                              63                              94
[1] 2 2
[1] FALSE
D63V8, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED   43 22
  DEL PEAK 33(13Q21.31) WILD-TYPE 80 21
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED     43   22
  DEL PEAK 33(13Q21.31) WILD-TYPE   80   21
     clus
vv    DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  NO                             43                              80
  YES                            22                              21
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED   26 43
  DEL PEAK 33(13Q21.31) WILD-TYPE 62 53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED     26   43
  DEL PEAK 33(13Q21.31) WILD-TYPE   62   53
                                   clus
vv                                  DEL PEAK 33(13Q21.31) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                26
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            43
                                   clus
vv                                  DEL PEAK 33(13Q21.31) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              53
[1] 2 2
[1] FALSE
D63V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 33(13Q21.31) MUTATED   55  1  1  2
  DEL PEAK 33(13Q21.31) WILD-TYPE 82 11  1  5
D63V12, multiclass
    clus
vv   DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  R0                            55                              82
  R1                             1                              11
  R2                             1                               1
  RX                             2                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q21.31) MUTATED      26                         2    36
  DEL PEAK 33(13Q21.31) WILD-TYPE    20                         3    78
D63V14, multiclass
                           clus
vv                          DEL PEAK 33(13Q21.31) MUTATED
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                36
                           clus
vv                          DEL PEAK 33(13Q21.31) WILD-TYPE
  ASIAN                                                  20
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED    3 37
  DEL PEAK 33(13Q21.31) WILD-TYPE  3 51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED      3   37
  DEL PEAK 33(13Q21.31) WILD-TYPE    3   51
                        clus
vv                       DEL PEAK 33(13Q21.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            37
                        clus
vv                       DEL PEAK 33(13Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              51
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 34(14Q23.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(14Q23.3) MUTATED   25 26
  DEL PEAK 34(14Q23.3) WILD-TYPE 83 50
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            51                            133 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            26                             50 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27         7.63         8.94        16.24         4.21        35.21 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH 
       23.41        12.82         4.67        14.50       122.10        47.38 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
       25.22         0.30        26.33         3.16        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A56G 
       15.48         3.75        55.50         2.66        16.47        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A7HV TCGA-LN-A7HY 
       10.36        10.45        13.25        12.59        10.52        12.03 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       33.11         7.59         5.06         6.35         9.30        15.78 
TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 
        7.00        25.81        22.82        12.43        18.31        52.27 
TCGA-VR-AA4G TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.05         2.66        19.73 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.12         5.16        20.02        25.78        14.30        58.55 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
        5.92        13.94        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.53        17.03         0.79         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH 
       31.56        24.03         6.28         3.16        30.25        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       58.59         4.90         7.43         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        3.02        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       46.09         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
       16.31         7.04        38.40        53.95         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27         8.98        27.09         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB 
        1.32 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                         12.82                          13.15 
[1] "0.3 - 122.1 (12.8)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.3"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         3        1        1        0         9
  DEL PEAK 34(14Q23.3) WILD-TYPE       5        4        5        1        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED           7         9          4          3
  DEL PEAK 34(14Q23.3) WILD-TYPE        24        16         10          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(14Q23.3) MUTATED            2        1         3
  DEL PEAK 34(14Q23.3) WILD-TYPE          5        4         1
D64V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             9                             38
  STAGE IIB                             7                             24
  STAGE III                             9                             16
  STAGE IIIA                            4                             10
  STAGE IIIB                            3                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 34(14Q23.3) MUTATED      10  7 28  1
  DEL PEAK 34(14Q23.3) WILD-TYPE    22 36 59  4
D64V4, multiclass
       clus
vv      DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T0+T1                           10                             22
  T2                               7                             36
  T3                              28                             59
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 34(14Q23.3) MUTATED   16 22  5  2
  DEL PEAK 34(14Q23.3) WILD-TYPE 61 46  7  6
D64V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           16                             61
  N1                           22                             46
  N2                            5                              7
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED    33   4
  DEL PEAK 34(14Q23.3) WILD-TYPE 102   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     33    4
  DEL PEAK 34(14Q23.3) WILD-TYPE  102    5
   clus
vv  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  0                           33                            102
  1                            4                              5
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     7  44
  DEL PEAK 34(14Q23.3) WILD-TYPE  20 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      7   44
  DEL PEAK 34(14Q23.3) WILD-TYPE   20  113
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                            7                             20
  MALE                             44                            113
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q23.3) MUTATED   35 10
  DEL PEAK 34(14Q23.3) WILD-TYPE 88 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     35   10
  DEL PEAK 34(14Q23.3) WILD-TYPE   88   33
     clus
vv    DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  NO                            35                             88
  YES                           10                             33
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q23.3) MUTATED   32 19
  DEL PEAK 34(14Q23.3) WILD-TYPE 56 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     32   19
  DEL PEAK 34(14Q23.3) WILD-TYPE   56   77
                                   clus
vv                                  DEL PEAK 34(14Q23.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               32
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           19
                                   clus
vv                                  DEL PEAK 34(14Q23.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 56
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             77
[1] 2 2
[1] FALSE
D64V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(14Q23.3) MUTATED    35   4   0   2
  DEL PEAK 34(14Q23.3) WILD-TYPE 102   8   2   5
D64V12, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  R0                           35                            102
  R1                            4                              8
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q23.3) MUTATED       8                         1    33
  DEL PEAK 34(14Q23.3) WILD-TYPE    38                         4    81
D64V14, multiclass
                           clus
vv                          DEL PEAK 34(14Q23.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               33
                           clus
vv                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                 38
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q23.3) MUTATED    1 18
  DEL PEAK 34(14Q23.3) WILD-TYPE  5 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      1   18
  DEL PEAK 34(14Q23.3) WILD-TYPE    5   70
                        clus
vv                       DEL PEAK 34(14Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       DEL PEAK 34(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             70
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 35(15Q11.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 35(15Q11.2) MUTATED   37 26
  DEL PEAK 35(15Q11.2) WILD-TYPE 71 50
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            63                            121 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            26                             50 
$`DEL PEAK 35(15Q11.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT 
       34.85        18.28         8.94        24.00         4.70        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
        5.16        20.02         7.63         5.92        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A625 TCGA-IG-A97H 
        7.69        35.21        20.12         3.88        12.82        14.50 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM 
       23.18        31.56        25.22         0.30        32.61        47.93 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        4.90        29.00         3.02        55.50         2.66        12.92 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49R 
        5.49         8.71        13.41        83.24        10.45        13.38 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        22.39        15.52        12.33        12.33        25.25 
TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ 
       12.03        13.38         0.13        12.85        12.26         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW 
        5.06        16.31        38.40         9.30         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-X8-AAAR 
        3.42        16.44        25.81        28.11        18.18        18.21 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       14.37         3.42         2.10 

$`DEL PEAK 35(15Q11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-L5-A8NG TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM 
       35.97        25.78        31.27        14.30        58.55        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        8.94         4.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        47.38        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.28         3.16        30.25        26.33        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.85        11.54        13.22         4.47        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       12.23        13.18        12.33        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.82         8.02         7.04         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        2.89         2.30        12.69         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        15.91        25.08        41.23         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                          0.13                           0.36 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                         13.38                          12.76 
[1] "0.1 - 83.2 (13.4)"  "0.4 - 122.1 (12.8)"
[1] "hr=" "1"  
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(15Q11.2) MUTATED         3        1        2        0        14
  DEL PEAK 35(15Q11.2) WILD-TYPE       5        4        4        1        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q11.2) MUTATED          10         8          5          5
  DEL PEAK 35(15Q11.2) WILD-TYPE        21        17          9          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(15Q11.2) MUTATED            2        2         3
  DEL PEAK 35(15Q11.2) WILD-TYPE          5        3         1
D65V3, multiclass
            clus
vv           DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            14                             33
  STAGE IIB                            10                             21
  STAGE III                             8                             17
  STAGE IIIA                            5                              9
  STAGE IIIB                            5                              4
  STAGE IIIC                            2                              5
  STAGE IV                              2                              3
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 35(15Q11.2) MUTATED      12 13 32  0
  DEL PEAK 35(15Q11.2) WILD-TYPE    20 30 55  5
D65V4, multiclass
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  T0+T1                           12                             20
  T2                              13                             30
  T3                              32                             55
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 35(15Q11.2) MUTATED   25 23  6  2
  DEL PEAK 35(15Q11.2) WILD-TYPE 52 45  6  6
D65V5, multiclass
    clus
vv   DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  N0                           25                             52
  N1                           23                             45
  N2                            6                              6
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED   45  5
  DEL PEAK 35(15Q11.2) WILD-TYPE 90  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED     45    5
  DEL PEAK 35(15Q11.2) WILD-TYPE   90    4
   clus
vv  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  0                           45                             90
  1                            5                              4
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(15Q11.2) MUTATED     8  55
  DEL PEAK 35(15Q11.2) WILD-TYPE  19 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      8   55
  DEL PEAK 35(15Q11.2) WILD-TYPE   19  102
        clus
vv       DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  FEMALE                            8                             19
  MALE                             55                            102
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED   46 12
  DEL PEAK 35(15Q11.2) WILD-TYPE 77 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED     46   12
  DEL PEAK 35(15Q11.2) WILD-TYPE   77   31
     clus
vv    DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  NO                            46                             77
  YES                           12                             31
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED   35 28
  DEL PEAK 35(15Q11.2) WILD-TYPE 53 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED     35   28
  DEL PEAK 35(15Q11.2) WILD-TYPE   53   68
                                   clus
vv                                  DEL PEAK 35(15Q11.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               35
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           28
                                   clus
vv                                  DEL PEAK 35(15Q11.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 53
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             68
[1] 2 2
[1] FALSE
D65V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 35(15Q11.2) MUTATED   43  7  0  4
  DEL PEAK 35(15Q11.2) WILD-TYPE 94  5  2  3
D65V12, multiclass
    clus
vv   DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  R0                           43                             94
  R1                            7                              5
  R2                            0                              2
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(15Q11.2) MUTATED      16                         2    38
  DEL PEAK 35(15Q11.2) WILD-TYPE    30                         3    76
D65V14, multiclass
                           clus
vv                          DEL PEAK 35(15Q11.2) MUTATED
  ASIAN                                               16
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               38
                           clus
vv                          DEL PEAK 35(15Q11.2) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED    2 32
  DEL PEAK 35(15Q11.2) WILD-TYPE  4 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      2   32
  DEL PEAK 35(15Q11.2) WILD-TYPE    4   56
                        clus
vv                       DEL PEAK 35(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       DEL PEAK 35(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             56
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 36(16P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 36(16P13.3) MUTATED   33 32
  DEL PEAK 36(16P13.3) WILD-TYPE 75 44
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            65                            119 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            32                             44 
$`DEL PEAK 36(16P13.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       34.85        18.28         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       27.12         5.16        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-JY-A6FH 
        8.94         4.21        32.45         7.69        20.12        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OR 
       23.18        25.22         3.16        32.61         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       58.59         7.40         3.75         3.02        12.92        13.48 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
        5.49        52.57        46.09        10.36        10.45        12.43 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HW TCGA-LN-A7HY 
       12.59        22.39        12.33         4.47        12.00        12.03 
TCGA-LN-A8HZ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
       12.33        12.26         8.02         5.06        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
        7.00         5.29         3.42        16.44         9.27        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JE 
       22.82        12.43        52.27        15.91         2.10 

$`DEL PEAK 36(16P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39         4.31        19.99        22.82        35.97 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IG-A3I8 
       20.02        25.78        31.27        14.30        16.24        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       44.75        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
       24.03         6.28        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93        18.35         3.32         7.17         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE 
        7.13         7.43        15.48         2.60        25.12        55.50 
TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        2.66        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        83.24        10.85         5.92        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        15.52        11.54        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       10.52        12.23        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.03        12.85        33.11         7.82         7.59        16.31 
TCGA-R6-A6L6 TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET 
        7.04        20.38        15.35         8.98        25.81         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         1.32         2.66        19.73 

  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                          0.36                           0.13 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         58.59                         122.10 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         12.26                          13.38 
[1] "0.4 - 58.6 (12.3)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.4"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(16P13.3) MUTATED         4        1        2        0         8
  DEL PEAK 36(16P13.3) WILD-TYPE       4        4        4        1        39
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16P13.3) MUTATED           9        11          6          4
  DEL PEAK 36(16P13.3) WILD-TYPE        22        14          8          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 36(16P13.3) MUTATED            1        2         1
  DEL PEAK 36(16P13.3) WILD-TYPE          6        3         3
D66V3, multiclass
            clus
vv           DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                             8                             39
  STAGE IIB                             9                             22
  STAGE III                            11                             14
  STAGE IIIA                            6                              8
  STAGE IIIB                            4                              5
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 36(16P13.3) MUTATED      13 10 28  2
  DEL PEAK 36(16P13.3) WILD-TYPE    19 33 59  3
D66V4, multiclass
       clus
vv      DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  T0+T1                           13                             19
  T2                              10                             33
  T3                              28                             59
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 36(16P13.3) MUTATED   18 28  6  1
  DEL PEAK 36(16P13.3) WILD-TYPE 59 40  6  7
D66V5, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  N0                           18                             59
  N1                           28                             40
  N2                            6                              6
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED   42  3
  DEL PEAK 36(16P13.3) WILD-TYPE 93  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     42    3
  DEL PEAK 36(16P13.3) WILD-TYPE   93    6
   clus
vv  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  0                           42                             93
  1                            3                              6
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED    7 58
  DEL PEAK 36(16P13.3) WILD-TYPE 20 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      7   58
  DEL PEAK 36(16P13.3) WILD-TYPE   20   99
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  FEMALE                            7                             20
  MALE                             58                             99
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED   48 12
  DEL PEAK 36(16P13.3) WILD-TYPE 75 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     48   12
  DEL PEAK 36(16P13.3) WILD-TYPE   75   31
     clus
vv    DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  NO                            48                             75
  YES                           12                             31
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED   46 19
  DEL PEAK 36(16P13.3) WILD-TYPE 42 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     46   19
  DEL PEAK 36(16P13.3) WILD-TYPE   42   77
                                   clus
vv                                  DEL PEAK 36(16P13.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               46
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           19
                                   clus
vv                                  DEL PEAK 36(16P13.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 42
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             77
[1] 2 2
[1] FALSE
D66V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 36(16P13.3) MUTATED   42  5  2  4
  DEL PEAK 36(16P13.3) WILD-TYPE 95  7  0  3
D66V12, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  R0                           42                             95
  R1                            5                              7
  R2                            2                              0
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16P13.3) MUTATED      11                         1    43
  DEL PEAK 36(16P13.3) WILD-TYPE    35                         4    71
D66V14, multiclass
                           clus
vv                          DEL PEAK 36(16P13.3) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               43
                           clus
vv                          DEL PEAK 36(16P13.3) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED    3 27
  DEL PEAK 36(16P13.3) WILD-TYPE  3 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      3   27
  DEL PEAK 36(16P13.3) WILD-TYPE    3   61
                        clus
vv                       DEL PEAK 36(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 36(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             61
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 37(16Q23.1) MUTATED   47 37
  DEL PEAK 37(16Q23.1) WILD-TYPE 61 39
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            84                            100 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            37                             39 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y 
       60.39        34.85        18.28         8.94        24.00         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       35.97        27.12        31.27         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS 
        8.94        16.24         4.21        35.21        20.12         3.88 
TCGA-IG-A50L TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
        0.53        14.50       122.10        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OR 
       25.22         3.16        26.33        21.01        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.75         3.02        55.50         2.66        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        7.76         5.49         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49W 
       10.85        10.36        10.45        13.41        12.59        13.25 
TCGA-LN-A4A1 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       12.59        12.33        13.22        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       13.18        12.85         8.02         7.59         5.06        16.31 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO 
       12.69         7.00         5.29        16.44         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       27.09        22.82        25.08         3.42         2.66        19.73 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU 
       15.68         4.31         4.70        19.99        22.82         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GR TCGA-IC-A6RE 
       20.02        25.78        14.30        58.55        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27         0.85        20.78         2.63        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       21.70        24.03         6.28        30.25         0.30        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88W 
       47.93         3.32         7.17         1.38        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NV 
        7.40        12.92        13.48        13.55        21.37        52.57 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        12.85        15.52        11.54         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       25.25        12.23        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.03        12.26        33.11         7.82         7.04        38.40 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35         8.98        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       41.23        14.37         2.10         1.32 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.36                           0.13 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        122.10                          68.02 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        12.770                         13.165 
[1] "0.4 - 122.1 (12.8)" "0.1 - 68.0 (13.2)" 
[1] "hr=" "1.1"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(16Q23.1) MUTATED         4        1        2        0        15
  DEL PEAK 37(16Q23.1) WILD-TYPE       4        4        4        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(16Q23.1) MUTATED          16        14          4          4
  DEL PEAK 37(16Q23.1) WILD-TYPE        15        11         10          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 37(16Q23.1) MUTATED            3        1         3
  DEL PEAK 37(16Q23.1) WILD-TYPE          4        4         1
D67V3, multiclass
            clus
vv           DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            15                             32
  STAGE IIB                            16                             15
  STAGE III                            14                             11
  STAGE IIIA                            4                             10
  STAGE IIIB                            4                              5
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 37(16Q23.1) MUTATED      14 16 41  0
  DEL PEAK 37(16Q23.1) WILD-TYPE    18 27 46  5
D67V4, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                           14                             18
  T2                              16                             27
  T3                              41                             46
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 37(16Q23.1) MUTATED   26 36  5  3
  DEL PEAK 37(16Q23.1) WILD-TYPE 51 32  7  5
D67V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           26                             51
  N1                           36                             32
  N2                            5                              7
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED   56  4
  DEL PEAK 37(16Q23.1) WILD-TYPE 79  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     56    4
  DEL PEAK 37(16Q23.1) WILD-TYPE   79    5
   clus
vv  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  0                           56                             79
  1                            4                              5
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED    9 75
  DEL PEAK 37(16Q23.1) WILD-TYPE 18 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      9   75
  DEL PEAK 37(16Q23.1) WILD-TYPE   18   82
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                            9                             18
  MALE                             75                             82
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED   59 15
  DEL PEAK 37(16Q23.1) WILD-TYPE 64 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     59   15
  DEL PEAK 37(16Q23.1) WILD-TYPE   64   28
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            59                             64
  YES                           15                             28
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED   62 22
  DEL PEAK 37(16Q23.1) WILD-TYPE 26 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     62   22
  DEL PEAK 37(16Q23.1) WILD-TYPE   26   74
                                   clus
vv                                  DEL PEAK 37(16Q23.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               62
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           22
                                   clus
vv                                  DEL PEAK 37(16Q23.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 26
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D67V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 37(16Q23.1) MUTATED   61  5  0  2
  DEL PEAK 37(16Q23.1) WILD-TYPE 76  7  2  5
D67V12, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  R0                           61                             76
  R1                            5                              7
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.1) MUTATED      15                         2    56
  DEL PEAK 37(16Q23.1) WILD-TYPE    31                         3    58
D67V14, multiclass
                           clus
vv                          DEL PEAK 37(16Q23.1) MUTATED
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               56
                           clus
vv                          DEL PEAK 37(16Q23.1) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED    4 33
  DEL PEAK 37(16Q23.1) WILD-TYPE  2 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      4   33
  DEL PEAK 37(16Q23.1) WILD-TYPE    2   55
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             55
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 38(17P12) MUTATION ANALYSIS
D68V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 38(17P12) MUTATED   48 38
  DEL PEAK 38(17P12) WILD-TYPE 60 38
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          86                           98 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          38                           38 
$`DEL PEAK 38(17P12) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        34.85        18.28        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GK 
       35.97        27.12         5.16        20.02        25.78         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A4P3 
        5.92        13.94         8.94         4.21        32.45        18.64 
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH 
        3.88         0.79        23.41        14.50       122.10        47.38 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       31.56        25.22        30.25        26.33        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        7.17         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
        3.75        55.50        13.48        16.47        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        83.24         5.92        10.45        12.66 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A7HV 
       13.15        15.35        13.25        12.59        12.33        10.52 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.18        12.33        12.85        33.11         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        5.06         7.04        38.40         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       12.69         7.00        20.38        16.44         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       18.18        46.19        11.24        18.21        25.08        14.37 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`DEL PEAK 38(17P12) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T TCGA-2H-A9GH 
       15.68         4.31         8.94        19.99        22.82        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       14.30        58.55        16.24         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L 
        0.85        20.78         2.63        20.12         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.03         6.28         3.16         0.30        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88W 
       18.35         1.38         3.16        58.59        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.40         3.02         2.66        12.92        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N 
       21.37        52.57        46.09        10.85        10.36        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        12.33        13.38        12.59        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
       12.26         8.02        16.31         6.35        53.95         2.89 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY 
        5.29         3.42        15.35        25.81        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD 
       52.27        18.05         9.17        15.91        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB 
        2.10         1.32 

  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                        0.36                         0.13 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      122.10                        68.02 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      13.200                       12.835 
[1] "0.4 - 122.1 (13.2)" "0.1 - 68.0 (12.8)" 
[1] "hr=" "1.1"
D68V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(17P12) MUTATED         5        1        3        0        17
  DEL PEAK 38(17P12) WILD-TYPE       3        4        3        1        30
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17P12) MUTATED          16        15          3          6
  DEL PEAK 38(17P12) WILD-TYPE        15        10         11          3
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 38(17P12) MUTATED            4        3         1
  DEL PEAK 38(17P12) WILD-TYPE          3        2         3
D68V3, multiclass
            clus
vv           DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  STAGE I                             5                            3
  STAGE IA                            1                            4
  STAGE IB                            3                            3
  STAGE II                            0                            1
  STAGE IIA                          17                           30
  STAGE IIB                          16                           15
  STAGE III                          15                           10
  STAGE IIIA                          3                           11
  STAGE IIIB                          6                            3
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           1                            3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 38(17P12) MUTATED      15 16 45  1
  DEL PEAK 38(17P12) WILD-TYPE    17 27 42  4
D68V4, multiclass
       clus
vv      DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  T0+T1                         15                           17
  T2                            16                           27
  T3                            45                           42
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 38(17P12) MUTATED   30 35  6  5
  DEL PEAK 38(17P12) WILD-TYPE 47 33  6  3
D68V5, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  N0                         30                           47
  N1                         35                           33
  N2                          6                            6
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED   63  4
  DEL PEAK 38(17P12) WILD-TYPE 72  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED     63    4
  DEL PEAK 38(17P12) WILD-TYPE   72    5
   clus
vv  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  0                         63                           72
  1                          4                            5
[1] 2 2
[1] FALSE
D68V7, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED    9 77
  DEL PEAK 38(17P12) WILD-TYPE 18 80
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      9   77
  DEL PEAK 38(17P12) WILD-TYPE   18   80
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  FEMALE                          9                           18
  MALE                           77                           80
[1] 2 2
[1] FALSE
D68V8, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED   56 20
  DEL PEAK 38(17P12) WILD-TYPE 67 23
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED     56   20
  DEL PEAK 38(17P12) WILD-TYPE   67   23
     clus
vv    DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  NO                          56                           67
  YES                         20                           23
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED   58 28
  DEL PEAK 38(17P12) WILD-TYPE 30 68
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED     58   28
  DEL PEAK 38(17P12) WILD-TYPE   30   68
                                   clus
vv                                  DEL PEAK 38(17P12) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                             58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                         28
                                   clus
vv                                  DEL PEAK 38(17P12) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                               30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           68
[1] 2 2
[1] FALSE
D68V11, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 38(17P12) MUTATED   59  7  0  3
  DEL PEAK 38(17P12) WILD-TYPE 78  5  2  4
D68V12, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  R0                         59                           78
  R1                          7                            5
  R2                          0                            2
  RX                          3                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17P12) MUTATED      14                         2    59
  DEL PEAK 38(17P12) WILD-TYPE    32                         3    55
D68V14, multiclass
                           clus
vv                          DEL PEAK 38(17P12) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             59
                           clus
vv                          DEL PEAK 38(17P12) WILD-TYPE
  ASIAN                                               32
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED    4 33
  DEL PEAK 38(17P12) WILD-TYPE  2 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      4   33
  DEL PEAK 38(17P12) WILD-TYPE    2   55
                        clus
vv                       DEL PEAK 38(17P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         33
                        clus
vv                       DEL PEAK 38(17P12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           55
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 39(17Q25.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 39(17Q25.3) MUTATED   33  8
  DEL PEAK 39(17Q25.3) WILD-TYPE 75 68
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            41                            143 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                             8                             68 
$`DEL PEAK 39(17Q25.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-2H-A9GN 
       34.85         4.70         0.36        35.97         5.16         8.94 
TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L5-A4OH 
        7.69        18.64         0.79        23.41        14.50        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
       21.01         3.16        29.00         7.40         3.75        55.50 
TCGA-L5-A8NR TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MQ 
        8.71        12.66        13.15        12.46        12.85        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-V5-A7RE 
        0.13        12.85         7.82         9.30        15.78        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-X8-AAAR 
       15.35         8.98        28.11        52.27        18.21 

$`DEL PEAK 39(17Q25.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH 
       19.99        22.82        27.12        20.02        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       30.25         0.30        26.33        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60        25.12         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.38        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       13.22         4.47        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
       16.31         7.04        38.40         6.35        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          0.13                           0.30 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          55.5                          122.1 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                         12.46                          13.22 
[1] "0.1 - 55.5 (12.5)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "2.2"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(17Q25.3) MUTATED         3        1        2        1        12
  DEL PEAK 39(17Q25.3) WILD-TYPE       5        4        4        0        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(17Q25.3) MUTATED           7         5          1          2
  DEL PEAK 39(17Q25.3) WILD-TYPE        24        20         13          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 39(17Q25.3) MUTATED            0        0         2
  DEL PEAK 39(17Q25.3) WILD-TYPE          7        5         2
D69V3, multiclass
            clus
vv           DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            12                             35
  STAGE IIB                             7                             24
  STAGE III                             5                             20
  STAGE IIIA                            1                             13
  STAGE IIIB                            2                              7
  STAGE IIIC                            0                              7
  STAGE IV                              0                              5
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 39(17Q25.3) MUTATED      10 10 19  0
  DEL PEAK 39(17Q25.3) WILD-TYPE    22 33 68  5
D69V4, multiclass
       clus
vv      DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  T0+T1                           10                             22
  T2                              10                             33
  T3                              19                             68
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 39(17Q25.3) MUTATED   21 15  2  0
  DEL PEAK 39(17Q25.3) WILD-TYPE 56 53 10  8
D69V5, multiclass
    clus
vv   DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  N0                           21                             56
  N1                           15                             53
  N2                            2                             10
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q25.3) MUTATED    33   2
  DEL PEAK 39(17Q25.3) WILD-TYPE 102   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED     33    2
  DEL PEAK 39(17Q25.3) WILD-TYPE  102    7
   clus
vv  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  0                           33                            102
  1                            2                              7
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q25.3) MUTATED     6  35
  DEL PEAK 39(17Q25.3) WILD-TYPE  21 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED      6   35
  DEL PEAK 39(17Q25.3) WILD-TYPE   21  122
        clus
vv       DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  FEMALE                            6                             21
  MALE                             35                            122
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                              0  1
  DEL PEAK 39(17Q25.3) MUTATED   29  8
  DEL PEAK 39(17Q25.3) WILD-TYPE 94 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED     29    8
  DEL PEAK 39(17Q25.3) WILD-TYPE   94   35
     clus
vv    DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  NO                            29                             94
  YES                            8                             35
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, binary
                                cls
clus                              0  1
  DEL PEAK 39(17Q25.3) MUTATED   19 22
  DEL PEAK 39(17Q25.3) WILD-TYPE 69 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED     19   22
  DEL PEAK 39(17Q25.3) WILD-TYPE   69   74
                                   clus
vv                                  DEL PEAK 39(17Q25.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               19
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           22
                                   clus
vv                                  DEL PEAK 39(17Q25.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 69
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             74
[1] 2 2
[1] FALSE
D69V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17Q25.3) MUTATED    34   0   0   2
  DEL PEAK 39(17Q25.3) WILD-TYPE 103  12   2   5
D69V12, multiclass
    clus
vv   DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  R0                           34                            103
  R1                            0                             12
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17Q25.3) MUTATED      14                         1    23
  DEL PEAK 39(17Q25.3) WILD-TYPE    32                         4    91
D69V14, multiclass
                           clus
vv                          DEL PEAK 39(17Q25.3) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               23
                           clus
vv                          DEL PEAK 39(17Q25.3) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                                cls
clus                              0  1
  DEL PEAK 39(17Q25.3) MUTATED    1 25
  DEL PEAK 39(17Q25.3) WILD-TYPE  5 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED      1   25
  DEL PEAK 39(17Q25.3) WILD-TYPE    5   63
                        clus
vv                       DEL PEAK 39(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 39(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             63
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 40(18P11.23) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 40(18P11.23) MUTATED   34 26
  DEL PEAK 40(18P11.23) WILD-TYPE 74 50
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             60                             124 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             26                              50 
$`DEL PEAK 40(18P11.23) MUTATED`
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       18.28        24.00         4.70        35.97         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 
       25.78        14.30         5.92         8.94        16.24        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.85         2.63         0.79        23.41        14.50        44.75 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22        24.03        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NE 
       26.33        32.61         7.17        15.48         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR 
        2.66        12.92        16.47        13.55        13.22         8.71 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 
       52.57         5.92        10.45        12.43        12.46        12.59 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG 
       12.03        13.18        12.85         7.82         7.59        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EP 
        6.35         9.30         2.30         7.00         9.27        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       22.82         8.12        18.21        41.23         3.42        19.73 

$`DEL PEAK 40(18P11.23) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       22.82         0.36        27.12        31.27        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA 
       13.94         4.21        32.45         7.69        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-KH-A6WC 
       68.02         3.68        41.52        47.38        21.70         6.28 
TCGA-L5-A43C TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.16        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NM 
        2.60        25.12         7.40         3.02        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
        5.49        21.37        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.36        12.66        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        12.59        13.25        12.62        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         8.02         5.06        16.31         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95        15.78         2.89        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        3.42        16.44        15.35         8.98        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         2.10         1.32         2.66 

  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           0.30                            0.13 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           55.5                           122.1 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                         13.200                          12.835 
[1] "0.3 - 55.5 (13.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D70V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(18P11.23) MUTATED         3        1        3        0        11
  DEL PEAK 40(18P11.23) WILD-TYPE       5        4        3        1        36
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18P11.23) MUTATED           7        11          5          6
  DEL PEAK 40(18P11.23) WILD-TYPE        24        14          9          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 40(18P11.23) MUTATED            2        1         2
  DEL PEAK 40(18P11.23) WILD-TYPE          5        4         2
D70V3, multiclass
            clus
vv           DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               4
  STAGE IB                               3                               3
  STAGE II                               0                               1
  STAGE IIA                             11                              36
  STAGE IIB                              7                              24
  STAGE III                             11                              14
  STAGE IIIA                             5                               9
  STAGE IIIB                             6                               3
  STAGE IIIC                             2                               5
  STAGE IV                               1                               4
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 40(18P11.23) MUTATED       9  8 36  1
  DEL PEAK 40(18P11.23) WILD-TYPE    23 35 51  4
D70V4, multiclass
       clus
vv      DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  T0+T1                             9                              23
  T2                                8                              35
  T3                               36                              51
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 40(18P11.23) MUTATED   22 23  6  2
  DEL PEAK 40(18P11.23) WILD-TYPE 55 45  6  6
D70V5, multiclass
    clus
vv   DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  N0                            22                              55
  N1                            23                              45
  N2                             6                               6
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED   43  3
  DEL PEAK 40(18P11.23) WILD-TYPE 92  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     43    3
  DEL PEAK 40(18P11.23) WILD-TYPE   92    6
   clus
vv  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  0                            43                              92
  1                             3                               6
[1] 2 2
[1] FALSE
D70V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.23) MUTATED    12  48
  DEL PEAK 40(18P11.23) WILD-TYPE  15 109
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     12   48
  DEL PEAK 40(18P11.23) WILD-TYPE   15  109
        clus
vv       DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  FEMALE                            12                              15
  MALE                              48                             109
[1] 2 2
[1] FALSE
D70V8, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED   45  7
  DEL PEAK 40(18P11.23) WILD-TYPE 78 36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     45    7
  DEL PEAK 40(18P11.23) WILD-TYPE   78   36
     clus
vv    DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  NO                             45                              78
  YES                             7                              36
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED   36 24
  DEL PEAK 40(18P11.23) WILD-TYPE 52 72
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     36   24
  DEL PEAK 40(18P11.23) WILD-TYPE   52   72
                                   clus
vv                                  DEL PEAK 40(18P11.23) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                36
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            24
                                   clus
vv                                  DEL PEAK 40(18P11.23) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  52
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              72
[1] 2 2
[1] FALSE
D70V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 40(18P11.23) MUTATED   40  7  0  3
  DEL PEAK 40(18P11.23) WILD-TYPE 97  5  2  4
D70V12, multiclass
    clus
vv   DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  R0                            40                              97
  R1                             7                               5
  R2                             0                               2
  RX                             3                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18P11.23) MUTATED      12                         0    42
  DEL PEAK 40(18P11.23) WILD-TYPE    34                         5    72
D70V14, multiclass
                           clus
vv                          DEL PEAK 40(18P11.23) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                42
                           clus
vv                          DEL PEAK 40(18P11.23) WILD-TYPE
  ASIAN                                                  34
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED    2 26
  DEL PEAK 40(18P11.23) WILD-TYPE  4 62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED      2   26
  DEL PEAK 40(18P11.23) WILD-TYPE    4   62
                        clus
vv                       DEL PEAK 40(18P11.23) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            26
                        clus
vv                       DEL PEAK 40(18P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              62
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 41(18Q12.2) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 41(18Q12.2) MUTATED   61 50
  DEL PEAK 41(18Q12.2) WILD-TYPE 47 26
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           111                             73 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            50                             26 
$`DEL PEAK 41(18Q12.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ 
       27.12         5.16        20.02        25.78        31.27        58.55 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45         7.69         0.85 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C 
       14.50        12.16        68.02         3.68        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        25.22        24.03         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       32.61         3.32         7.17         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43        15.48         2.60         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 
       12.33        13.38        15.35        13.25        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.85        12.33        13.22         4.47        12.23        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.38        13.18        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        8.02         7.59         6.35        53.95         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP 
       12.69         7.00         5.29         3.42         9.27        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D 
       22.82        12.43        18.31         8.12        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.66        19.73 

$`DEL PEAK 41(18Q12.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3QL 
       14.30         7.63         5.92        13.94        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.78        20.12        18.64         9.30        17.03        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A939 
       14.86         4.67       122.10        44.75        41.52        21.70 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        6.28        30.25        21.01        47.93        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
       58.59        25.12         7.40         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        5.92        13.15        12.59        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        12.59        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FR 
       10.52        12.00        12.03        12.33         0.13        12.26 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31         7.04        38.40         9.30        15.78 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET 
       20.38        16.44        15.35         8.98        25.81         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JE 
       28.11        33.70        52.27        11.24        14.37         2.10 
TCGA-Z6-A9VB 
        1.32 

  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         12.85                          13.94 
[1] "0.3 - 83.2 (12.8)"  "0.1 - 122.1 (13.9)"
[1] "hr=" "1.4"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(18Q12.2) MUTATED         4        2        3        1        26
  DEL PEAK 41(18Q12.2) WILD-TYPE       4        3        3        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q12.2) MUTATED          17        17          7          7
  DEL PEAK 41(18Q12.2) WILD-TYPE        14         8          7          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 41(18Q12.2) MUTATED            6        4         2
  DEL PEAK 41(18Q12.2) WILD-TYPE          1        1         2
D71V3, multiclass
            clus
vv           DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            26                             21
  STAGE IIB                            17                             14
  STAGE III                            17                              8
  STAGE IIIA                            7                              7
  STAGE IIIB                            7                              2
  STAGE IIIC                            6                              1
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 41(18Q12.2) MUTATED      16 24 57  3
  DEL PEAK 41(18Q12.2) WILD-TYPE    16 19 30  2
D71V4, multiclass
       clus
vv      DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  T0+T1                           16                             16
  T2                              24                             19
  T3                              57                             30
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 41(18Q12.2) MUTATED   44 40  9  6
  DEL PEAK 41(18Q12.2) WILD-TYPE 33 28  3  2
D71V5, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  N0                           44                             33
  N1                           40                             28
  N2                            9                              3
  N3                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   81  6
  DEL PEAK 41(18Q12.2) WILD-TYPE 54  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     81    6
  DEL PEAK 41(18Q12.2) WILD-TYPE   54    3
   clus
vv  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  0                           81                             54
  1                            6                              3
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   17 94
  DEL PEAK 41(18Q12.2) WILD-TYPE 10 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     17   94
  DEL PEAK 41(18Q12.2) WILD-TYPE   10   63
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  FEMALE                           17                             10
  MALE                             94                             63
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   74 25
  DEL PEAK 41(18Q12.2) WILD-TYPE 49 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     74   25
  DEL PEAK 41(18Q12.2) WILD-TYPE   49   18
     clus
vv    DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  NO                            74                             49
  YES                           25                             18
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   61 50
  DEL PEAK 41(18Q12.2) WILD-TYPE 27 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     61   50
  DEL PEAK 41(18Q12.2) WILD-TYPE   27   46
                                   clus
vv                                  DEL PEAK 41(18Q12.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           50
                                   clus
vv                                  DEL PEAK 41(18Q12.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 27
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             46
[1] 2 2
[1] FALSE
D71V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 41(18Q12.2) MUTATED   79  9  2  4
  DEL PEAK 41(18Q12.2) WILD-TYPE 58  3  0  3
D71V12, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  R0                           79                             58
  R1                            9                              3
  R2                            2                              0
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q12.2) MUTATED      25                         3    69
  DEL PEAK 41(18Q12.2) WILD-TYPE    21                         2    45
D71V14, multiclass
                           clus
vv                          DEL PEAK 41(18Q12.2) MUTATED
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               69
                           clus
vv                          DEL PEAK 41(18Q12.2) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED    4 47
  DEL PEAK 41(18Q12.2) WILD-TYPE  2 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED      4   47
  DEL PEAK 41(18Q12.2) WILD-TYPE    2   41
                        clus
vv                       DEL PEAK 41(18Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 41(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             41
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 42(18Q21.2) MUTATED   68 51
  DEL PEAK 42(18Q21.2) WILD-TYPE 40 25
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           119                             65 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            51                             25 
$`DEL PEAK 42(18Q21.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       58.55         7.63        13.94         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        7.69         0.85         2.63        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        47.38        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.16         0.30        26.33        32.61        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         3.16         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        83.24        52.57        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W 
       12.66        12.43        13.41        12.33        13.38        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.59        22.39        12.85        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 
        4.47        12.33        25.25        12.23        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00         5.29        16.44         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43        18.31         8.12 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.66        19.73 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
        5.92         4.21        33.27        35.21        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        9.30        17.03        12.82        14.86         4.67       122.10 
TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OM 
       44.75        41.52        21.70         6.28        30.25        47.93 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A88Z 
       18.35         1.38        58.59         7.13        25.12         7.40 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
        7.76         5.49        46.09         5.92        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
       12.59        12.62        12.49        12.76        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       11.54        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-S8-A6BW 
        0.13         5.06        16.31         7.04        15.78        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
        3.42        15.35         8.98         1.55        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.18        52.27        11.24         2.10         1.32 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         13.18                          12.82 
[1] "0.3 - 83.2 (13.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(18Q21.2) MUTATED         5        2        4        1        27
  DEL PEAK 42(18Q21.2) WILD-TYPE       3        3        2        0        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q21.2) MUTATED          21        18          7          7
  DEL PEAK 42(18Q21.2) WILD-TYPE        10         7          7          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 42(18Q21.2) MUTATED            5        4         2
  DEL PEAK 42(18Q21.2) WILD-TYPE          2        1         2
D72V3, multiclass
            clus
vv           DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              3
  STAGE IB                              4                              2
  STAGE II                              1                              0
  STAGE IIA                            27                             20
  STAGE IIB                            21                             10
  STAGE III                            18                              7
  STAGE IIIA                            7                              7
  STAGE IIIB                            7                              2
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 42(18Q21.2) MUTATED      20 26 58  3
  DEL PEAK 42(18Q21.2) WILD-TYPE    12 17 29  2
D72V4, multiclass
       clus
vv      DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  T0+T1                           20                             12
  T2                              26                             17
  T3                              58                             29
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 42(18Q21.2) MUTATED   47 45  9  5
  DEL PEAK 42(18Q21.2) WILD-TYPE 30 23  3  3
D72V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  N0                           47                             30
  N1                           45                             23
  N2                            9                              3
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   88  6
  DEL PEAK 42(18Q21.2) WILD-TYPE 47  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     88    6
  DEL PEAK 42(18Q21.2) WILD-TYPE   47    3
   clus
vv  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  0                           88                             47
  1                            6                              3
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED    17 102
  DEL PEAK 42(18Q21.2) WILD-TYPE  10  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     17  102
  DEL PEAK 42(18Q21.2) WILD-TYPE   10   55
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  FEMALE                           17                             10
  MALE                            102                             55
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   78 29
  DEL PEAK 42(18Q21.2) WILD-TYPE 45 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     78   29
  DEL PEAK 42(18Q21.2) WILD-TYPE   45   14
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  NO                            78                             45
  YES                           29                             14
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   66 53
  DEL PEAK 42(18Q21.2) WILD-TYPE 22 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     66   53
  DEL PEAK 42(18Q21.2) WILD-TYPE   22   43
                                   clus
vv                                  DEL PEAK 42(18Q21.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           53
                                   clus
vv                                  DEL PEAK 42(18Q21.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 22
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             43
[1] 2 2
[1] FALSE
D72V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 42(18Q21.2) MUTATED   87  9  2  4
  DEL PEAK 42(18Q21.2) WILD-TYPE 50  3  0  3
D72V12, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  R0                           87                             50
  R1                            9                              3
  R2                            2                              0
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q21.2) MUTATED      27                         3    74
  DEL PEAK 42(18Q21.2) WILD-TYPE    19                         2    40
D72V14, multiclass
                           clus
vv                          DEL PEAK 42(18Q21.2) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               74
                           clus
vv                          DEL PEAK 42(18Q21.2) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED    6 51
  DEL PEAK 42(18Q21.2) WILD-TYPE  0 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      6   51
  DEL PEAK 42(18Q21.2) WILD-TYPE    0   37
                        clus
vv                       DEL PEAK 42(18Q21.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       DEL PEAK 42(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             37
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 43(18Q22.3) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 43(18Q22.3) MUTATED   67 45
  DEL PEAK 43(18Q22.3) WILD-TYPE 41 31
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           112                             72 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            45                             31 
$`DEL PEAK 43(18Q22.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        25.78        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        7.63         8.94        16.24        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85         2.63        18.64         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       47.38        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR 
        0.30        26.33        32.61        21.01         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        4.90        29.00         7.43        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.85        10.36        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.38        13.25        12.46        12.59        12.85        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 
       13.22         4.47        12.33        12.23        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.59        38.40         6.35         9.30         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        7.00         5.29         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       12.43        18.31         8.12        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       14.37         3.42         2.10        19.73 

$`DEL PEAK 43(18Q22.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YA 
       58.55         5.92        13.94         4.21        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.12         3.88         9.30        17.03        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E 
        4.67       122.10        41.52        21.70         6.28        30.25 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
       47.93        18.35         7.17         1.38        58.59         7.13 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
       25.12         7.40        13.48         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        5.92        10.45        13.15        15.35        12.59        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 
        0.13         5.06        16.31         7.04        53.95        15.78 
TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        2.89        20.38         3.42        16.44        15.35         8.98 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.55        28.11        18.18        11.24         1.32         2.66 

  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                         13.20                          12.79 
[1] "0.3 - 83.2 (13.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q22.3) MUTATED         4        1        3        1        25
  DEL PEAK 43(18Q22.3) WILD-TYPE       4        4        3        0        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q22.3) MUTATED          21        17          9          6
  DEL PEAK 43(18Q22.3) WILD-TYPE        10         8          5          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 43(18Q22.3) MUTATED            5        4         2
  DEL PEAK 43(18Q22.3) WILD-TYPE          2        1         2
D73V3, multiclass
            clus
vv           DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            25                             22
  STAGE IIB                            21                             10
  STAGE III                            17                              8
  STAGE IIIA                            9                              5
  STAGE IIIB                            6                              3
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 43(18Q22.3) MUTATED      16 24 59  3
  DEL PEAK 43(18Q22.3) WILD-TYPE    16 19 28  2
D73V4, multiclass
       clus
vv      DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  T0+T1                           16                             16
  T2                              24                             19
  T3                              59                             28
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 43(18Q22.3) MUTATED   42 46  8  5
  DEL PEAK 43(18Q22.3) WILD-TYPE 35 22  4  3
D73V5, multiclass
    clus
vv   DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  N0                           42                             35
  N1                           46                             22
  N2                            8                              4
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   84  6
  DEL PEAK 43(18Q22.3) WILD-TYPE 51  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     84    6
  DEL PEAK 43(18Q22.3) WILD-TYPE   51    3
   clus
vv  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  0                           84                             51
  1                            6                              3
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   18 94
  DEL PEAK 43(18Q22.3) WILD-TYPE  9 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     18   94
  DEL PEAK 43(18Q22.3) WILD-TYPE    9   63
        clus
vv       DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  FEMALE                           18                              9
  MALE                             94                             63
[1] 2 2
[1] FALSE
D73V8, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   74 27
  DEL PEAK 43(18Q22.3) WILD-TYPE 49 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     74   27
  DEL PEAK 43(18Q22.3) WILD-TYPE   49   16
     clus
vv    DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  NO                            74                             49
  YES                           27                             16
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   58 54
  DEL PEAK 43(18Q22.3) WILD-TYPE 30 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     58   54
  DEL PEAK 43(18Q22.3) WILD-TYPE   30   42
                                   clus
vv                                  DEL PEAK 43(18Q22.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               58
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           54
                                   clus
vv                                  DEL PEAK 43(18Q22.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 30
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             42
[1] 2 2
[1] FALSE
D73V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 43(18Q22.3) MUTATED   80 10  2  5
  DEL PEAK 43(18Q22.3) WILD-TYPE 57  2  0  2
D73V12, multiclass
    clus
vv   DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  R0                           80                             57
  R1                           10                              2
  R2                            2                              0
  RX                            5                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q22.3) MUTATED      25                         3    71
  DEL PEAK 43(18Q22.3) WILD-TYPE    21                         2    43
D73V14, multiclass
                           clus
vv                          DEL PEAK 43(18Q22.3) MUTATED
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               71
                           clus
vv                          DEL PEAK 43(18Q22.3) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED    6 45
  DEL PEAK 43(18Q22.3) WILD-TYPE  0 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED      6   45
  DEL PEAK 43(18Q22.3) WILD-TYPE    0   43
                        clus
vv                       DEL PEAK 43(18Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       DEL PEAK 43(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             43
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 44(19P13.3) MUTATED   55 39
  DEL PEAK 44(19P13.3) WILD-TYPE 53 37
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            94                             90 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            39                             37 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y TCGA-L5-A8NG TCGA-2H-A9GF 
       34.85         8.94        24.00         0.36        35.97        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       16.24         4.21         2.63        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       17.03         0.79        23.41         4.67        14.50       122.10 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF 
       68.02        47.38        23.18        25.22        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX 
       32.61        47.93         3.32         7.17        58.59         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60         3.75         2.66        12.92        16.47        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        5.49         8.71        13.41        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45        12.66        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.49        12.76        12.85        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
        4.47        12.33        10.52        12.23        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 
       13.18         0.13        12.26         8.02         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40         6.35        15.78         2.89         2.30        12.69 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        3.42        16.44         9.27        25.81        27.09        12.43 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
        8.12        52.27        46.19         9.17        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         2.10         2.66        19.73 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GL TCGA-2H-A9GR 
       22.82        27.12         5.16        20.02         5.92        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69        33.27        35.21         0.85        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA 
        9.30        12.82         9.96        14.86        12.16        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.16         0.30        21.01        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13        15.48        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50        13.48        13.22         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49V 
       83.24         5.92        12.43        13.41        12.33        12.59 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.59        12.59        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FP 
       13.22        25.25        12.00        12.03        12.33        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 
       12.85        33.11         7.82         7.59        16.31        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX 
        9.30         7.00        20.38         5.29        15.35         8.98 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82         1.55        18.31        28.11        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.05        11.24        18.21        41.23         3.42         1.32 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.13                           0.30 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        12.885                         13.220 
[1] "0.1 - 122.1 (12.9)" "0.3 - 83.2 (13.2)" 
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         4        2        3        1        18
  DEL PEAK 44(19P13.3) WILD-TYPE       4        3        3        0        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          16        16          5          6
  DEL PEAK 44(19P13.3) WILD-TYPE        15         9          9          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 44(19P13.3) MUTATED            4        2         3
  DEL PEAK 44(19P13.3) WILD-TYPE          3        3         1
D74V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            18                             29
  STAGE IIB                            16                             15
  STAGE III                            16                              9
  STAGE IIIA                            5                              9
  STAGE IIIB                            6                              3
  STAGE IIIC                            4                              3
  STAGE IV                              2                              3
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 44(19P13.3) MUTATED      16 17 48  2
  DEL PEAK 44(19P13.3) WILD-TYPE    16 26 39  3
D74V4, multiclass
       clus
vv      DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T0+T1                           16                             16
  T2                              17                             26
  T3                              48                             39
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 44(19P13.3) MUTATED   33 38  7  4
  DEL PEAK 44(19P13.3) WILD-TYPE 44 30  5  4
D74V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           33                             44
  N1                           38                             30
  N2                            7                              5
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED   69  5
  DEL PEAK 44(19P13.3) WILD-TYPE 66  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     69    5
  DEL PEAK 44(19P13.3) WILD-TYPE   66    4
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                           69                             66
  1                            5                              4
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED    9 85
  DEL PEAK 44(19P13.3) WILD-TYPE 18 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      9   85
  DEL PEAK 44(19P13.3) WILD-TYPE   18   72
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                            9                             18
  MALE                             85                             72
[1] 2 2
[1] FALSE
D74V8, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED   57 26
  DEL PEAK 44(19P13.3) WILD-TYPE 66 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     57   26
  DEL PEAK 44(19P13.3) WILD-TYPE   66   17
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                            57                             66
  YES                           26                             17
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED   50 44
  DEL PEAK 44(19P13.3) WILD-TYPE 38 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     50   44
  DEL PEAK 44(19P13.3) WILD-TYPE   38   52
                                   clus
vv                                  DEL PEAK 44(19P13.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               50
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           44
                                   clus
vv                                  DEL PEAK 44(19P13.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 38
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             52
[1] 2 2
[1] FALSE
D74V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 44(19P13.3) MUTATED   68  4  2  4
  DEL PEAK 44(19P13.3) WILD-TYPE 69  8  0  3
D74V12, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                           68                             69
  R1                            4                              8
  R2                            2                              0
  RX                            4                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED      26                         4    51
  DEL PEAK 44(19P13.3) WILD-TYPE    20                         1    63
D74V14, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               51
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED    3 44
  DEL PEAK 44(19P13.3) WILD-TYPE  3 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      3   44
  DEL PEAK 44(19P13.3) WILD-TYPE    3   44
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             44
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 45(20P12.1) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 45(20P12.1) MUTATED   22 11
  DEL PEAK 45(20P12.1) WILD-TYPE 86 65
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            33                            151 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            11                             65 
$`DEL PEAK 45(20P12.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD 
       34.85         8.94        14.30         3.88        44.75        68.02 
TCGA-JY-A6FH TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NE TCGA-L5-A8NF 
       47.38        26.33        32.61         3.32        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY 
       10.45        12.66        13.41        12.46        12.00        12.03 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EQ 
        5.06        38.40        53.95        12.69        20.38        22.82 
TCGA-VR-A8Q7 TCGA-XP-A8T8 TCGA-ZR-A9CJ 
       52.27        14.37        19.73 

$`DEL PEAK 45(20P12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.02        25.78        31.27        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
      122.10         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH 
        2.60        25.12         7.40         3.75         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV 
       13.48        13.55         7.76         5.49        21.37        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       46.09        10.85         5.92        12.43        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02         7.59        16.31         7.04         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         2.30         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                          2.66                           0.13 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                         14.30                          12.82 
[1] "2.7 - 83.2 (14.3)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "2"  
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(20P12.1) MUTATED         1        0        1        0         7
  DEL PEAK 45(20P12.1) WILD-TYPE       7        5        5        1        40
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(20P12.1) MUTATED           7         6          1          1
  DEL PEAK 45(20P12.1) WILD-TYPE        24        19         13          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 45(20P12.1) MUTATED            3        0         1
  DEL PEAK 45(20P12.1) WILD-TYPE          4        5         3
D75V3, multiclass
            clus
vv           DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              5
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             7                             40
  STAGE IIB                             7                             24
  STAGE III                             6                             19
  STAGE IIIA                            1                             13
  STAGE IIIB                            1                              8
  STAGE IIIC                            3                              4
  STAGE IV                              0                              5
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 45(20P12.1) MUTATED       4  8 17  0
  DEL PEAK 45(20P12.1) WILD-TYPE    28 35 70  5
D75V4, multiclass
       clus
vv      DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  T0+T1                            4                             28
  T2                               8                             35
  T3                              17                             70
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 45(20P12.1) MUTATED   12 12  2  3
  DEL PEAK 45(20P12.1) WILD-TYPE 65 56 10  5
D75V5, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  N0                           12                             65
  N1                           12                             56
  N2                            2                             10
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED    23   1
  DEL PEAK 45(20P12.1) WILD-TYPE 112   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     23    1
  DEL PEAK 45(20P12.1) WILD-TYPE  112    8
   clus
vv  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  0                           23                            112
  1                            1                              8
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED     3  30
  DEL PEAK 45(20P12.1) WILD-TYPE  24 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED      3   30
  DEL PEAK 45(20P12.1) WILD-TYPE   24  127
        clus
vv       DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  FEMALE                            3                             24
  MALE                             30                            127
[1] 2 2
[1] FALSE
D75V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED    23   7
  DEL PEAK 45(20P12.1) WILD-TYPE 100  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     23    7
  DEL PEAK 45(20P12.1) WILD-TYPE  100   36
     clus
vv    DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  NO                            23                            100
  YES                            7                             36
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, binary
                                cls
clus                              0  1
  DEL PEAK 45(20P12.1) MUTATED   22 11
  DEL PEAK 45(20P12.1) WILD-TYPE 66 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     22   11
  DEL PEAK 45(20P12.1) WILD-TYPE   66   85
                                   clus
vv                                  DEL PEAK 45(20P12.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               22
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           11
                                   clus
vv                                  DEL PEAK 45(20P12.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 66
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             85
[1] 2 2
[1] FALSE
D75V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(20P12.1) MUTATED    27   0   0   1
  DEL PEAK 45(20P12.1) WILD-TYPE 110  12   2   6
D75V12, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  R0                           27                            110
  R1                            0                             12
  R2                            0                              2
  RX                            1                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(20P12.1) MUTATED       8                         1    21
  DEL PEAK 45(20P12.1) WILD-TYPE    38                         4    93
D75V14, multiclass
                           clus
vv                          DEL PEAK 45(20P12.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               21
                           clus
vv                          DEL PEAK 45(20P12.1) WILD-TYPE
  ASIAN                                                 38
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                                cls
clus                              0  1
  DEL PEAK 45(20P12.1) MUTATED    2 13
  DEL PEAK 45(20P12.1) WILD-TYPE  4 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED      2   13
  DEL PEAK 45(20P12.1) WILD-TYPE    4   75
                        clus
vv                       DEL PEAK 45(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       DEL PEAK 45(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             75
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 46(21Q21.1) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 46(21Q21.1) MUTATED   62 45
  DEL PEAK 46(21Q21.1) WILD-TYPE 46 31
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                           107                             77 
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                            45                             31 
$`DEL PEAK 46(21Q21.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR 
       27.12        25.78         7.63         5.92        13.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
        0.53         0.79         9.96        12.16       122.10        68.02 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        0.30        26.33        32.61        47.93         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         5.49         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       52.57        46.09        10.85        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.41        13.38        13.15        13.25        12.76        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22         4.47        12.33        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       12.03        13.18        13.38        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.89         2.30        12.69         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D 
        8.12        28.11        18.18        52.27        46.19         9.17 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         2.10         2.66        19.73 

$`DEL PEAK 46(21Q21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39        34.85        19.99        22.82        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN 
        5.16        20.02        31.27        14.30        58.55         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT 
       16.24         4.21         7.69        35.21         2.63         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03        23.41        12.82        14.86         4.67        14.50 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-KH-A6WC 
       44.75         3.68        41.52        47.38        21.70         6.28 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88W TCGA-L5-A8NE 
       21.01        18.35         3.32         1.38        25.12        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       13.48         7.76        21.37        83.24        10.45        12.66 
TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.33        15.35        12.59        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
       12.49        12.59        22.39        15.52        11.54        25.25 
TCGA-LN-A7HV TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6DQ 
       10.52        12.33        13.18         0.13        12.03         7.59 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       16.31        53.95        15.78         7.00        20.38         5.29 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B 
       15.35        27.09        18.31        33.70        18.05        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21        25.08         3.42         1.32 

  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE 
                         12.43                          15.35 
[1] "0.3 - 122.1 (12.4)" "0.1 - 83.2 (15.3)" 
[1] "hr=" "1.2"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(21Q21.1) MUTATED         5        3        5        1        22
  DEL PEAK 46(21Q21.1) WILD-TYPE       3        2        1        0        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(21Q21.1) MUTATED          15        16          8          5
  DEL PEAK 46(21Q21.1) WILD-TYPE        16         9          6          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 46(21Q21.1) MUTATED            5        3         2
  DEL PEAK 46(21Q21.1) WILD-TYPE          2        2         2
D76V3, multiclass
            clus
vv           DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              3                              2
  STAGE IB                              5                              1
  STAGE II                              1                              0
  STAGE IIA                            22                             25
  STAGE IIB                            15                             16
  STAGE III                            16                              9
  STAGE IIIA                            8                              6
  STAGE IIIB                            5                              4
  STAGE IIIC                            5                              2
  STAGE IV                              3                              2
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 46(21Q21.1) MUTATED      18 20 52  3
  DEL PEAK 46(21Q21.1) WILD-TYPE    14 23 35  2
D76V4, multiclass
       clus
vv      DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  T0+T1                           18                             14
  T2                              20                             23
  T3                              52                             35
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 46(21Q21.1) MUTATED   42 40  6  5
  DEL PEAK 46(21Q21.1) WILD-TYPE 35 28  6  3
D76V5, multiclass
    clus
vv   DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  N0                           42                             35
  N1                           40                             28
  N2                            6                              6
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                                cls
clus                              0  1
  DEL PEAK 46(21Q21.1) MUTATED   75  5
  DEL PEAK 46(21Q21.1) WILD-TYPE 60  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q21.1) MUTATED     75    5
  DEL PEAK 46(21Q21.1) WILD-TYPE   60    4
   clus
vv  DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  0                           75                             60
  1                            5                              4
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                              0  1
  DEL PEAK 46(21Q21.1) MUTATED   14 93
  DEL PEAK 46(21Q21.1) WILD-TYPE 13 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q21.1) MUTATED     14   93
  DEL PEAK 46(21Q21.1) WILD-TYPE   13   64
        clus
vv       DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  FEMALE                           14                             13
  MALE                             93                             64
[1] 2 2
[1] FALSE
D76V8, binary
                                cls
clus                              0  1
  DEL PEAK 46(21Q21.1) MUTATED   71 25
  DEL PEAK 46(21Q21.1) WILD-TYPE 52 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q21.1) MUTATED     71   25
  DEL PEAK 46(21Q21.1) WILD-TYPE   52   18
     clus
vv    DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  NO                            71                             52
  YES                           25                             18
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, binary
                                cls
clus                              0  1
  DEL PEAK 46(21Q21.1) MUTATED   57 50
  DEL PEAK 46(21Q21.1) WILD-TYPE 31 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q21.1) MUTATED     57   50
  DEL PEAK 46(21Q21.1) WILD-TYPE   31   46
                                   clus
vv                                  DEL PEAK 46(21Q21.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               57
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           50
                                   clus
vv                                  DEL PEAK 46(21Q21.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             46
[1] 2 2
[1] FALSE
D76V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 46(21Q21.1) MUTATED   74 10  1  5
  DEL PEAK 46(21Q21.1) WILD-TYPE 63  2  1  2
D76V12, multiclass
    clus
vv   DEL PEAK 46(21Q21.1) MUTATED DEL PEAK 46(21Q21.1) WILD-TYPE
  R0                           74                             63
  R1                           10                              2
  R2                            1                              1
  RX                            5                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(21Q21.1) MUTATED      23                         3    69
  DEL PEAK 46(21Q21.1) WILD-TYPE    23                         2    45
D76V14, multiclass
                           clus
vv                          DEL PEAK 46(21Q21.1) MUTATED
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               69
                           clus
vv                          DEL PEAK 46(21Q21.1) WILD-TYPE
  ASIAN                                                 23
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                                cls
clus                              0  1
  DEL PEAK 46(21Q21.1) MUTATED    4 45
  DEL PEAK 46(21Q21.1) WILD-TYPE  2 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q21.1) MUTATED      4   45
  DEL PEAK 46(21Q21.1) WILD-TYPE    2   43
                        clus
vv                       DEL PEAK 46(21Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       DEL PEAK 46(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             43
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 47(21Q22.12) MUTATION ANALYSIS
D77V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 47(21Q22.12) MUTATED   62 46
  DEL PEAK 47(21Q22.12) WILD-TYPE 46 30
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                            108                              76 
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                             46                              30 
$`DEL PEAK 47(21Q22.12) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
        4.31         8.94        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       27.12        25.78         7.63         5.92        13.94         8.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45        33.27         0.85        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA 
        3.88         0.53         0.79         9.96       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       68.02        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        0.30        32.61        21.01        47.93         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       16.47        13.55        13.22         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.36         5.92        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.15        12.62        12.76        12.85        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.38        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06         7.04        38.40         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        2.89         2.30        12.69         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        8.98        25.81        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        52.27        46.19        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23        14.37         2.10         2.66        19.73 

$`DEL PEAK 47(21Q22.12) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO 
        5.16        20.02        31.27        14.30        58.55        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
        4.21         7.69        35.21         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
        3.68        41.52        47.38        21.70        25.22         6.28 
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88W TCGA-L5-A8NE 
       26.33        18.35         3.32         1.38        25.12        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       13.48         7.76         5.49        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.66        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.46        12.59        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I1 TCGA-LN-A9FO 
       11.54         4.47        25.25        10.52        13.18         0.13 
TCGA-LN-A9FP TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW 
       12.03        16.31        53.95        15.78         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G 
        5.29        15.35        27.09        18.31        33.70        18.05 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21         3.42         1.32 

  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                           0.30                            0.13 
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                         122.10                           83.24 
  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE 
                         12.430                          15.105 
[1] "0.3 - 122.1 (12.4)" "0.1 - 83.2 (15.1)" 
[1] "hr=" "1.2"
D77V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q22.12) MUTATED         6        3        5        1        23
  DEL PEAK 47(21Q22.12) WILD-TYPE       2        2        1        0        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q22.12) MUTATED          16        15          6          5
  DEL PEAK 47(21Q22.12) WILD-TYPE        15        10          8          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 47(21Q22.12) MUTATED            5        3         2
  DEL PEAK 47(21Q22.12) WILD-TYPE          2        2         2
D77V3, multiclass
            clus
vv           DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  STAGE I                                6                               2
  STAGE IA                               3                               2
  STAGE IB                               5                               1
  STAGE II                               1                               0
  STAGE IIA                             23                              24
  STAGE IIB                             16                              15
  STAGE III                             15                              10
  STAGE IIIA                             6                               8
  STAGE IIIB                             5                               4
  STAGE IIIC                             5                               2
  STAGE IV                               3                               2
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 47(21Q22.12) MUTATED      18 22 50  3
  DEL PEAK 47(21Q22.12) WILD-TYPE    14 21 37  2
D77V4, multiclass
       clus
vv      DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  T0+T1                            18                              14
  T2                               22                              21
  T3                               50                              37
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 47(21Q22.12) MUTATED   44 37  6  6
  DEL PEAK 47(21Q22.12) WILD-TYPE 33 31  6  2
D77V5, multiclass
    clus
vv   DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  N0                            44                              33
  N1                            37                              31
  N2                             6                               6
  N3                             6                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                                 cls
clus                               0  1
  DEL PEAK 47(21Q22.12) MUTATED   77  5
  DEL PEAK 47(21Q22.12) WILD-TYPE 58  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(21Q22.12) MUTATED     77    5
  DEL PEAK 47(21Q22.12) WILD-TYPE   58    4
   clus
vv  DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  0                            77                              58
  1                             5                               4
[1] 2 2
[1] FALSE
D77V7, binary
                                 cls
clus                               0  1
  DEL PEAK 47(21Q22.12) MUTATED   17 91
  DEL PEAK 47(21Q22.12) WILD-TYPE 10 66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(21Q22.12) MUTATED     17   91
  DEL PEAK 47(21Q22.12) WILD-TYPE   10   66
        clus
vv       DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  FEMALE                            17                              10
  MALE                              91                              66
[1] 2 2
[1] FALSE
D77V8, binary
                                 cls
clus                               0  1
  DEL PEAK 47(21Q22.12) MUTATED   73 23
  DEL PEAK 47(21Q22.12) WILD-TYPE 50 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(21Q22.12) MUTATED     73   23
  DEL PEAK 47(21Q22.12) WILD-TYPE   50   20
     clus
vv    DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  NO                             73                              50
  YES                            23                              20
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, binary
                                 cls
clus                               0  1
  DEL PEAK 47(21Q22.12) MUTATED   57 51
  DEL PEAK 47(21Q22.12) WILD-TYPE 31 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(21Q22.12) MUTATED     57   51
  DEL PEAK 47(21Q22.12) WILD-TYPE   31   45
                                   clus
vv                                  DEL PEAK 47(21Q22.12) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                                57
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            51
                                   clus
vv                                  DEL PEAK 47(21Q22.12) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                  31
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                              45
[1] 2 2
[1] FALSE
D77V11, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 47(21Q22.12) MUTATED   78  9  0  5
  DEL PEAK 47(21Q22.12) WILD-TYPE 59  3  2  2
D77V12, multiclass
    clus
vv   DEL PEAK 47(21Q22.12) MUTATED DEL PEAK 47(21Q22.12) WILD-TYPE
  R0                            78                              59
  R1                             9                               3
  R2                             0                               2
  RX                             5                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q22.12) MUTATED      23                         4    68
  DEL PEAK 47(21Q22.12) WILD-TYPE    23                         1    46
D77V14, multiclass
                           clus
vv                          DEL PEAK 47(21Q22.12) MUTATED
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                68
                           clus
vv                          DEL PEAK 47(21Q22.12) WILD-TYPE
  ASIAN                                                  23
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                                 cls
clus                               0  1
  DEL PEAK 47(21Q22.12) MUTATED    5 45
  DEL PEAK 47(21Q22.12) WILD-TYPE  1 43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(21Q22.12) MUTATED      5   45
  DEL PEAK 47(21Q22.12) WILD-TYPE    1   43
                        clus
vv                       DEL PEAK 47(21Q22.12) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            45
                        clus
vv                       DEL PEAK 47(21Q22.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              43
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 48(22Q11.1) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 48(22Q11.1) MUTATED   41 38
  DEL PEAK 48(22Q11.1) WILD-TYPE 67 38
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                            79                            105 
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                            38                             38 
$`DEL PEAK 48(22Q11.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-2H-A9GF 
       34.85        18.28        24.00         4.70         0.36        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB TCGA-IG-A4P3 
        8.94        16.24         4.21        32.45         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-JY-A6FH 
        3.88         0.53         0.79        23.41       122.10        47.38 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       31.56         3.16        32.61        18.35         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z 
       58.59         4.90        29.00         7.13         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW 
       16.47        13.55        13.22         5.49         8.71        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         5.92        10.45        13.41        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.25        12.62        12.76        10.52        12.03        13.18 
TCGA-LN-A8I1 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 
       13.18         8.02         7.59         5.06        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO 
        2.30         7.00         5.29        16.44         9.27        25.81 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       22.82        18.31        18.18        14.37         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`DEL PEAK 48(22Q11.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-IC-A6RE TCGA-IG-A3I8 
       35.97        27.12         5.16        20.02         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
       35.21         0.85        20.78        20.12         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88S 
       21.01        47.93         3.32         1.38         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       25.12         7.76        21.37        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V 
       10.85        12.66        12.43        12.33        13.15        12.59 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       25.25        12.00        12.23        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       12.03        12.85        12.26        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WG 
        7.04        38.40         6.35        53.95         9.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER 
       20.38         3.42        15.35         8.98        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       41.23         3.42         1.32 

  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                          0.36                           0.13 
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE 
                         12.92                          13.15 
[1] "0.4 - 122.1 (12.9)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.6"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(22Q11.1) MUTATED         5        2        3        0        14
  DEL PEAK 48(22Q11.1) WILD-TYPE       3        3        3        1        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(22Q11.1) MUTATED          12        17          4          2
  DEL PEAK 48(22Q11.1) WILD-TYPE        19         8         10          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 48(22Q11.1) MUTATED            4        3         3
  DEL PEAK 48(22Q11.1) WILD-TYPE          3        2         1
D78V3, multiclass
            clus
vv           DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              3
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                            14                             33
  STAGE IIB                            12                             19
  STAGE III                            17                              8
  STAGE IIIA                            4                             10
  STAGE IIIB                            2                              7
  STAGE IIIC                            4                              3
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 48(22Q11.1) MUTATED      19 11 42  0
  DEL PEAK 48(22Q11.1) WILD-TYPE    13 32 45  5
D78V4, multiclass
       clus
vv      DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  T0+T1                           19                             13
  T2                              11                             32
  T3                              42                             45
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 48(22Q11.1) MUTATED   27 39  2  4
  DEL PEAK 48(22Q11.1) WILD-TYPE 50 29 10  4
D78V5, multiclass
    clus
vv   DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  N0                           27                             50
  N1                           39                             29
  N2                            2                             10
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                                cls
clus                              0  1
  DEL PEAK 48(22Q11.1) MUTATED   56  6
  DEL PEAK 48(22Q11.1) WILD-TYPE 79  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(22Q11.1) MUTATED     56    6
  DEL PEAK 48(22Q11.1) WILD-TYPE   79    3
   clus
vv  DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  0                           56                             79
  1                            6                              3
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                              0  1
  DEL PEAK 48(22Q11.1) MUTATED   12 67
  DEL PEAK 48(22Q11.1) WILD-TYPE 15 90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(22Q11.1) MUTATED     12   67
  DEL PEAK 48(22Q11.1) WILD-TYPE   15   90
        clus
vv       DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  FEMALE                           12                             15
  MALE                             67                             90
[1] 2 2
[1] FALSE
D78V8, binary
                                cls
clus                              0  1
  DEL PEAK 48(22Q11.1) MUTATED   48 20
  DEL PEAK 48(22Q11.1) WILD-TYPE 75 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(22Q11.1) MUTATED     48   20
  DEL PEAK 48(22Q11.1) WILD-TYPE   75   23
     clus
vv    DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  NO                            48                             75
  YES                           20                             23
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, binary
                                cls
clus                              0  1
  DEL PEAK 48(22Q11.1) MUTATED   54 25
  DEL PEAK 48(22Q11.1) WILD-TYPE 34 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(22Q11.1) MUTATED     54   25
  DEL PEAK 48(22Q11.1) WILD-TYPE   34   71
                                   clus
vv                                  DEL PEAK 48(22Q11.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               54
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           25
                                   clus
vv                                  DEL PEAK 48(22Q11.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 34
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             71
[1] 2 2
[1] FALSE
D78V11, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 48(22Q11.1) MUTATED   60  7  0  2
  DEL PEAK 48(22Q11.1) WILD-TYPE 77  5  2  5
D78V12, multiclass
    clus
vv   DEL PEAK 48(22Q11.1) MUTATED DEL PEAK 48(22Q11.1) WILD-TYPE
  R0                           60                             77
  R1                            7                              5
  R2                            0                              2
  RX                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(22Q11.1) MUTATED      13                         1    51
  DEL PEAK 48(22Q11.1) WILD-TYPE    33                         4    63
D78V14, multiclass
                           clus
vv                          DEL PEAK 48(22Q11.1) MUTATED
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               51
                           clus
vv                          DEL PEAK 48(22Q11.1) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                                cls
clus                              0  1
  DEL PEAK 48(22Q11.1) MUTATED    2 30
  DEL PEAK 48(22Q11.1) WILD-TYPE  4 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(22Q11.1) MUTATED      2   30
  DEL PEAK 48(22Q11.1) WILD-TYPE    4   58
                        clus
vv                       DEL PEAK 48(22Q11.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 48(22Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             58
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 49(XP21.1) MUTATION ANALYSIS
D79V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 49(XP21.1) MUTATED   41 29
  DEL PEAK 49(XP21.1) WILD-TYPE 67 47
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           70                           114 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           29                            47 
$`DEL PEAK 49(XP21.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78        14.30         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78         3.88         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C 
       12.82         9.96         4.67        44.75        47.38        23.18 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P 
        3.75        16.47        13.41         5.92        12.66        12.33 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR 
       13.38        12.46        12.59        12.49        22.39        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.33        25.25        10.52        12.00        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A8W8 
        0.13        12.85        12.26        33.11         8.02         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        2.30        12.69         5.29         9.27         8.98        25.81 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR 
       18.31         8.12        18.18        52.27        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       25.08        14.37         3.42         2.10 

$`DEL PEAK 49(XP21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.36        35.97        27.12        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3YB 
        5.92        13.94         8.94        16.24         7.69         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H 
       20.12        18.64         9.30         0.79        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        0.30        32.61         3.32         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33         4.47        12.23        12.03        12.33        13.18 
TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.03         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       38.40         6.35        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38         3.42        16.44        15.35        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43         1.55        28.11        33.70        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        41.23         1.32         2.66        19.73 

  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                        52.27                        122.10 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                       13.200                        12.885 
[1] "0.1 - 52.3 (13.2)"  "0.3 - 122.1 (12.9)"
[1] "hr=" "1.1"
D79V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(XP21.1) MUTATED         1        2        0        0        20
  DEL PEAK 49(XP21.1) WILD-TYPE       7        3        6        1        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(XP21.1) MUTATED          15         6          8          7
  DEL PEAK 49(XP21.1) WILD-TYPE        16        19          6          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 49(XP21.1) MUTATED            1        1         0
  DEL PEAK 49(XP21.1) WILD-TYPE          6        4         4
D79V3, multiclass
            clus
vv           DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                           20                            27
  STAGE IIB                           15                            16
  STAGE III                            6                            19
  STAGE IIIA                           8                             6
  STAGE IIIB                           7                             2
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 49(XP21.1) MUTATED      10 17 34  3
  DEL PEAK 49(XP21.1) WILD-TYPE    22 26 53  2
D79V4, multiclass
       clus
vv      DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  T0+T1                          10                            22
  T2                             17                            26
  T3                             34                            53
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 49(XP21.1) MUTATED   31 24  8  1
  DEL PEAK 49(XP21.1) WILD-TYPE 46 44  4  7
D79V5, multiclass
    clus
vv   DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  N0                          31                            46
  N1                          24                            44
  N2                           8                             4
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                               cls
clus                             0  1
  DEL PEAK 49(XP21.1) MUTATED   52  1
  DEL PEAK 49(XP21.1) WILD-TYPE 83  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED     52    1
  DEL PEAK 49(XP21.1) WILD-TYPE   83    8
   clus
vv  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  0                          52                            83
  1                           1                             8
[1] 2 2
[1] FALSE
D79V7, binary
                               cls
clus                             0  1
  DEL PEAK 49(XP21.1) MUTATED    6 64
  DEL PEAK 49(XP21.1) WILD-TYPE 21 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED      6   64
  DEL PEAK 49(XP21.1) WILD-TYPE   21   93
        clus
vv       DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  FEMALE                           6                            21
  MALE                            64                            93
[1] 2 2
[1] FALSE
D79V8, binary
                               cls
clus                             0  1
  DEL PEAK 49(XP21.1) MUTATED   47 13
  DEL PEAK 49(XP21.1) WILD-TYPE 76 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED     47   13
  DEL PEAK 49(XP21.1) WILD-TYPE   76   30
     clus
vv    DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  NO                           47                            76
  YES                          13                            30
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, binary
                               cls
clus                             0  1
  DEL PEAK 49(XP21.1) MUTATED   28 42
  DEL PEAK 49(XP21.1) WILD-TYPE 60 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED     28   42
  DEL PEAK 49(XP21.1) WILD-TYPE   60   54
                                   clus
vv                                  DEL PEAK 49(XP21.1) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              28
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          42
                                   clus
vv                                  DEL PEAK 49(XP21.1) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                60
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            54
[1] 2 2
[1] FALSE
D79V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 49(XP21.1) MUTATED   49  4  1  5
  DEL PEAK 49(XP21.1) WILD-TYPE 88  8  1  2
D79V12, multiclass
    clus
vv   DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  R0                          49                            88
  R1                           4                             8
  R2                           1                             1
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(XP21.1) MUTATED      24                         2    38
  DEL PEAK 49(XP21.1) WILD-TYPE    22                         3    76
D79V14, multiclass
                           clus
vv                          DEL PEAK 49(XP21.1) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              38
                           clus
vv                          DEL PEAK 49(XP21.1) WILD-TYPE
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                               cls
clus                             0  1
  DEL PEAK 49(XP21.1) MUTATED    4 39
  DEL PEAK 49(XP21.1) WILD-TYPE  2 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED      4   39
  DEL PEAK 49(XP21.1) WILD-TYPE    2   49
                        clus
vv                       DEL PEAK 49(XP21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       DEL PEAK 49(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            49
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 50(XP11.3) MUTATION ANALYSIS
D80V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 50(XP11.3) MUTATED   47 28
  DEL PEAK 50(XP11.3) WILD-TYPE 61 48
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                           75                           109 
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                           28                            48 
$`DEL PEAK 50(XP11.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        14.30         8.94         4.21        32.45        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.79        23.41        12.82         9.96         4.67        44.75 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       47.38        23.18        26.33        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K 
        7.17         3.75        16.47         8.71        13.41         5.92 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.33        13.38        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        12.49        22.39        11.54        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A8W8 
       13.18         0.13        12.85        12.26        33.11         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        2.30        12.69         9.27         8.98        25.81        27.09 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.31         8.12        52.27        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       14.37         3.42         2.10 

$`DEL PEAK 50(XP11.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.36        35.97        27.12        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YB 
        5.92        13.94        16.24         7.69        33.27         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       18.64         9.30        14.86        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         0.30        32.61 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76         5.49        21.37        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.36        10.45        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.15        15.35        12.59        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A8HZ TCGA-LN-A9FP 
       15.52        12.33         4.47        12.33        12.33        12.03 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       38.40         6.35        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EQ 
       20.38         5.29         3.42        16.44        15.35        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       12.43         1.55        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.05        11.24         9.17        41.23         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                         0.13                          0.30 
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                        52.27                        122.10 
  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE 
                        13.18                         12.92 
[1] "0.1 - 52.3 (13.2)"  "0.3 - 122.1 (12.9)"
[1] "hr=" "1"  
D80V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(XP11.3) MUTATED         1        2        1        0        23
  DEL PEAK 50(XP11.3) WILD-TYPE       7        3        5        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(XP11.3) MUTATED          14        10          8          8
  DEL PEAK 50(XP11.3) WILD-TYPE        17        15          6          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 50(XP11.3) MUTATED            0        1         0
  DEL PEAK 50(XP11.3) WILD-TYPE          7        4         4
D80V3, multiclass
            clus
vv           DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           23                            24
  STAGE IIB                           14                            17
  STAGE III                           10                            15
  STAGE IIIA                           8                             6
  STAGE IIIB                           8                             1
  STAGE IIIC                           0                             7
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 50(XP11.3) MUTATED       9 18 40  3
  DEL PEAK 50(XP11.3) WILD-TYPE    23 25 47  2
D80V4, multiclass
       clus
vv      DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  T0+T1                           9                            23
  T2                             18                            25
  T3                             40                            47
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 50(XP11.3) MUTATED   35 27  8  0
  DEL PEAK 50(XP11.3) WILD-TYPE 42 41  4  8
D80V5, multiclass
    clus
vv   DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  N0                          35                            42
  N1                          27                            41
  N2                           8                             4
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                               cls
clus                             0  1
  DEL PEAK 50(XP11.3) MUTATED   60  1
  DEL PEAK 50(XP11.3) WILD-TYPE 75  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP11.3) MUTATED     60    1
  DEL PEAK 50(XP11.3) WILD-TYPE   75    8
   clus
vv  DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  0                          60                            75
  1                           1                             8
[1] 2 2
[1] FALSE
D80V7, binary
                               cls
clus                             0  1
  DEL PEAK 50(XP11.3) MUTATED    7 68
  DEL PEAK 50(XP11.3) WILD-TYPE 20 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP11.3) MUTATED      7   68
  DEL PEAK 50(XP11.3) WILD-TYPE   20   89
        clus
vv       DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  FEMALE                           7                            20
  MALE                            68                            89
[1] 2 2
[1] FALSE
D80V8, binary
                               cls
clus                             0  1
  DEL PEAK 50(XP11.3) MUTATED   50 16
  DEL PEAK 50(XP11.3) WILD-TYPE 73 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP11.3) MUTATED     50   16
  DEL PEAK 50(XP11.3) WILD-TYPE   73   27
     clus
vv    DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  NO                           50                            73
  YES                          16                            27
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, binary
                               cls
clus                             0  1
  DEL PEAK 50(XP11.3) MUTATED   27 48
  DEL PEAK 50(XP11.3) WILD-TYPE 61 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP11.3) MUTATED     27   48
  DEL PEAK 50(XP11.3) WILD-TYPE   61   48
                                   clus
vv                                  DEL PEAK 50(XP11.3) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              27
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          48
                                   clus
vv                                  DEL PEAK 50(XP11.3) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                61
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            48
[1] 2 2
[1] FALSE
D80V11, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 50(XP11.3) MUTATED   56  3  1  5
  DEL PEAK 50(XP11.3) WILD-TYPE 81  9  1  2
D80V12, multiclass
    clus
vv   DEL PEAK 50(XP11.3) MUTATED DEL PEAK 50(XP11.3) WILD-TYPE
  R0                          56                            81
  R1                           3                             9
  R2                           1                             1
  RX                           5                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(XP11.3) MUTATED      29                         2    37
  DEL PEAK 50(XP11.3) WILD-TYPE    17                         3    77
D80V14, multiclass
                           clus
vv                          DEL PEAK 50(XP11.3) MUTATED
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              37
                           clus
vv                          DEL PEAK 50(XP11.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                               cls
clus                             0  1
  DEL PEAK 50(XP11.3) MUTATED    3 43
  DEL PEAK 50(XP11.3) WILD-TYPE  3 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP11.3) MUTATED      3   43
  DEL PEAK 50(XP11.3) WILD-TYPE    3   45
                        clus
vv                       DEL PEAK 50(XP11.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          43
                        clus
vv                       DEL PEAK 50(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            45
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 51(XQ11.2) MUTATION ANALYSIS
D81V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 51(XQ11.2) MUTATED   29 14
  DEL PEAK 51(XQ11.2) WILD-TYPE 79 62
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                           43                           141 
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                           14                            62 
$`DEL PEAK 51(XQ11.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-2H-A9GF 
       34.85         8.94        24.00         0.36         5.16        25.78 
TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C 
        4.21        20.12         9.96        44.75        47.38        23.18 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ 
       26.33        21.01         7.17         3.75        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.55         8.71        13.41         5.92        10.45        12.66 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I0 
       12.46        12.49        22.39        25.25        10.52        13.38 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC 
       12.85        33.11         7.82         2.30         5.29         3.42 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 
        9.27         8.98        25.81        11.24        18.21        25.08 
TCGA-Z6-AAPN 
        2.66 

$`DEL PEAK 51(XQ11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI 
       22.82        35.97        27.12        20.02        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.30        32.61        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        12.92        13.22         7.76         5.49        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N 
       83.24        52.57        46.09        10.85        10.36        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.25        12.62        12.59        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        12.03        12.26         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
       15.78         2.89        12.69         7.00        20.38        16.44 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       15.35        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        2.10         1.32        19.73 

  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                         0.36                          0.13 
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                        47.38                        122.10 
  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE 
                        12.66                         13.18 
[1] "0.4 - 47.4 (12.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D81V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XQ11.2) MUTATED         1        1        0        0        14
  DEL PEAK 51(XQ11.2) WILD-TYPE       7        4        6        1        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XQ11.2) MUTATED           7         5          1          4
  DEL PEAK 51(XQ11.2) WILD-TYPE        24        20         13          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 51(XQ11.2) MUTATED            0        1         0
  DEL PEAK 51(XQ11.2) WILD-TYPE          7        4         4
D81V3, multiclass
            clus
vv           DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             4
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                           14                            33
  STAGE IIB                            7                            24
  STAGE III                            5                            20
  STAGE IIIA                           1                            13
  STAGE IIIB                           4                             5
  STAGE IIIC                           0                             7
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 51(XQ11.2) MUTATED       6 10 23  0
  DEL PEAK 51(XQ11.2) WILD-TYPE    26 33 64  5
D81V4, multiclass
       clus
vv      DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  T0+T1                           6                            26
  T2                             10                            33
  T3                             23                            64
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 51(XQ11.2) MUTATED   19 14  5  1
  DEL PEAK 51(XQ11.2) WILD-TYPE 58 54  7  7
D81V5, multiclass
    clus
vv   DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  N0                          19                            58
  N1                          14                            54
  N2                           5                             7
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                               cls
clus                              0   1
  DEL PEAK 51(XQ11.2) MUTATED    31   1
  DEL PEAK 51(XQ11.2) WILD-TYPE 104   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XQ11.2) MUTATED     31    1
  DEL PEAK 51(XQ11.2) WILD-TYPE  104    8
   clus
vv  DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  0                          31                           104
  1                           1                             8
[1] 2 2
[1] FALSE
D81V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XQ11.2) MUTATED     7  36
  DEL PEAK 51(XQ11.2) WILD-TYPE  20 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XQ11.2) MUTATED      7   36
  DEL PEAK 51(XQ11.2) WILD-TYPE   20  121
        clus
vv       DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  FEMALE                           7                            20
  MALE                            36                           121
[1] 2 2
[1] FALSE
D81V8, binary
                               cls
clus                             0  1
  DEL PEAK 51(XQ11.2) MUTATED   29  8
  DEL PEAK 51(XQ11.2) WILD-TYPE 94 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XQ11.2) MUTATED     29    8
  DEL PEAK 51(XQ11.2) WILD-TYPE   94   35
     clus
vv    DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  NO                           29                            94
  YES                           8                            35
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, binary
                               cls
clus                             0  1
  DEL PEAK 51(XQ11.2) MUTATED   23 20
  DEL PEAK 51(XQ11.2) WILD-TYPE 65 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XQ11.2) MUTATED     23   20
  DEL PEAK 51(XQ11.2) WILD-TYPE   65   76
                                   clus
vv                                  DEL PEAK 51(XQ11.2) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                              23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                          20
                                   clus
vv                                  DEL PEAK 51(XQ11.2) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                            76
[1] 2 2
[1] FALSE
D81V11, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XQ11.2) MUTATED    31   2   0   4
  DEL PEAK 51(XQ11.2) WILD-TYPE 106  10   2   3
D81V12, multiclass
    clus
vv   DEL PEAK 51(XQ11.2) MUTATED DEL PEAK 51(XQ11.2) WILD-TYPE
  R0                          31                           106
  R1                           2                            10
  R2                           0                             2
  RX                           4                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XQ11.2) MUTATED      12                         2    23
  DEL PEAK 51(XQ11.2) WILD-TYPE    34                         3    91
D81V14, multiclass
                           clus
vv                          DEL PEAK 51(XQ11.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              23
                           clus
vv                          DEL PEAK 51(XQ11.2) WILD-TYPE
  ASIAN                                                34
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                               cls
clus                             0  1
  DEL PEAK 51(XQ11.2) MUTATED    2 20
  DEL PEAK 51(XQ11.2) WILD-TYPE  4 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XQ11.2) MUTATED      2   20
  DEL PEAK 51(XQ11.2) WILD-TYPE    4   68
                        clus
vv                       DEL PEAK 51(XQ11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK 51(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            68
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 52(XQ21.33) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 52(XQ21.33) MUTATED   27 14
  DEL PEAK 52(XQ21.33) WILD-TYPE 81 62
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            41                            143 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                            14                             62 
$`DEL PEAK 52(XQ21.33) MUTATED`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A88Y TCGA-2H-A9GF 
       15.68        34.85        18.28         8.94         0.36        25.78 
TCGA-2H-A9GQ TCGA-JY-A6FH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        4.21        47.38        21.01        47.93         7.17         3.16 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49M 
        3.75        13.48        16.47        13.55        13.22        12.66 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25        12.46        12.49        22.39        12.85        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ 
       25.25        10.52        12.03         0.13        33.11         5.06 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        2.89         2.30         7.00         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-ZR-A9CJ 
        8.98        25.81        11.24        25.08        19.73 

$`DEL PEAK 52(XQ21.33) WILD-TYPE`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       60.39         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GH TCGA-2H-A9GI 
       35.97        27.12         5.16        20.02        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61        18.35         3.32         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NM 
        7.40         3.02        55.50         2.66        12.92         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.62        12.59        12.76        12.59        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22         4.47        12.33        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18        12.03        12.85        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
        6.35        53.95         9.30        15.78        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        5.29        15.35        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       46.19        18.05         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       14.37         3.42         2.10         1.32         2.66 

  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                          0.13                           0.30 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                         47.93                         122.10 
  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE 
                         12.66                          13.18 
[1] "0.1 - 47.9 (12.7)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1"  
D82V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XQ21.33) MUTATED         1        4        1        1        11
  DEL PEAK 52(XQ21.33) WILD-TYPE       7        1        5        0        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XQ21.33) MUTATED           4         7          1          0
  DEL PEAK 52(XQ21.33) WILD-TYPE        27        18         13          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 52(XQ21.33) MUTATED            1        1         0
  DEL PEAK 52(XQ21.33) WILD-TYPE          6        4         4
D82V3, multiclass
            clus
vv           DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              4                              1
  STAGE IB                              1                              5
  STAGE II                              1                              0
  STAGE IIA                            11                             36
  STAGE IIB                             4                             27
  STAGE III                             7                             18
  STAGE IIIA                            1                             13
  STAGE IIIB                            0                              9
  STAGE IIIC                            1                              6
  STAGE IV                              1                              4
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 52(XQ21.33) MUTATED       8  9 18  0
  DEL PEAK 52(XQ21.33) WILD-TYPE    24 34 69  5
D82V4, multiclass
       clus
vv      DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  T0+T1                            8                             24
  T2                               9                             34
  T3                              18                             69
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 52(XQ21.33) MUTATED   20 12  1  2
  DEL PEAK 52(XQ21.33) WILD-TYPE 57 56 11  6
D82V5, multiclass
    clus
vv   DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  N0                           20                             57
  N1                           12                             56
  N2                            1                             11
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED    27   1
  DEL PEAK 52(XQ21.33) WILD-TYPE 108   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     27    1
  DEL PEAK 52(XQ21.33) WILD-TYPE  108    8
   clus
vv  DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  0                           27                            108
  1                            1                              8
[1] 2 2
[1] FALSE
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 52(XQ21.33) MUTATED     8  33
  DEL PEAK 52(XQ21.33) WILD-TYPE  19 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED      8   33
  DEL PEAK 52(XQ21.33) WILD-TYPE   19  124
        clus
vv       DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  FEMALE                            8                             19
  MALE                             33                            124
[1] 2 2
[1] FALSE
D82V8, binary
                                cls
clus                              0  1
  DEL PEAK 52(XQ21.33) MUTATED   25  9
  DEL PEAK 52(XQ21.33) WILD-TYPE 98 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     25    9
  DEL PEAK 52(XQ21.33) WILD-TYPE   98   34
     clus
vv    DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  NO                            25                             98
  YES                            9                             34
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, binary
                                cls
clus                              0  1
  DEL PEAK 52(XQ21.33) MUTATED   23 18
  DEL PEAK 52(XQ21.33) WILD-TYPE 65 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED     23   18
  DEL PEAK 52(XQ21.33) WILD-TYPE   65   78
                                   clus
vv                                  DEL PEAK 52(XQ21.33) MUTATED
  ESOPHAGUS ADENOCARCINOMA, NOS                               23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                           18
                                   clus
vv                                  DEL PEAK 52(XQ21.33) WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                                 65
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                             78
[1] 2 2
[1] FALSE
D82V11, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 52(XQ21.33) MUTATED    30   3   0   1
  DEL PEAK 52(XQ21.33) WILD-TYPE 107   9   2   6
D82V12, multiclass
    clus
vv   DEL PEAK 52(XQ21.33) MUTATED DEL PEAK 52(XQ21.33) WILD-TYPE
  R0                           30                            107
  R1                            3                              9
  R2                            0                              2
  RX                            1                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XQ21.33) MUTATED      11                         2    24
  DEL PEAK 52(XQ21.33) WILD-TYPE    35                         3    90
D82V14, multiclass
                           clus
vv                          DEL PEAK 52(XQ21.33) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               24
                           clus
vv                          DEL PEAK 52(XQ21.33) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                                cls
clus                              0  1
  DEL PEAK 52(XQ21.33) MUTATED    1 20
  DEL PEAK 52(XQ21.33) WILD-TYPE  5 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(XQ21.33) MUTATED      1   20
  DEL PEAK 52(XQ21.33) WILD-TYPE    5   68
                        clus
vv                       DEL PEAK 52(XQ21.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       DEL PEAK 52(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             68
[1] 2 2
[1] FALSE
